title: Neuron_oxBS_100

city: Piscataway

first: Alison

middle: I

last: Bernstein

state: NJ

address: 170 Freylinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject  99-63

hyb_protocol: To perform the assay, converted DNA was denatured with 0.4 N sodium hydroxide. Denatured DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using fluorophore-labeled nucleotides per the manufacturers protocol.

scan_protocol: Array BeadChips were scanned on the Illumina iScan platform.

data_processing:
Importing and annotation of data: Data was imported in using minfi (version 1.48.0) and annotation was set to the latest version of the EPIC array annotations (ilm10b4.hg19).
Quality control: Quality control was assessed for internal control probes using the ENmix (version 1.38.01) plotCtrl function.
Filtering probes: Probe-level detection p-values were identified and failed probes were identified as those with a detection p-value > 0.01 in any sample. Samples with >10% failed probes were removed from downstream analyses. Failed probes were removed from remaining samples when detection p-value was > 0.01 in > 5% of samples.
Removing cross-reactive and SNP probes: Cross-reactive probes and probes containing SNPs were removed based upon previous identification (Chen 2013; Zhou 2017).
Dye-bias correction: After removal of technical artifacts, dye-bias correction was performed with ssNoob within minfi (version 1.48.0).
Quality control and correcting for batch and positional effects: Batch effects were assessed using the ChAMP (version 2.32.0) package, and then a β value matrix for all samples was corrected for batch and positional effects using the posibatch (version 1.0) package for BS and oxBS samples.
Filtering samples: All female samples were removed due to small sample size and lack of statistical power after previous QC and filtering steps.
Estimating cell type proportions: The proportion of neuronal vs. glial cells in each sample was estimated with CETS from BS-derived beta values (version 3.03). Samples with estimated glial cell to neuronal cell proportion > 0.50 were removed from analysis.
Estimating beta values: 5-mC and 5-hmC beta values were estimated with oxBS.MLE in Enmix (version 1.38.01).
Filtering probes: Probes with mean βmC or βhmC < 0.01 across all samples were removed and a data set with probes common between the 5-mC and 5-hmC sets was created.
Average beta values after data processing steps for samples and probes remaining after data processing steps

source_name: parietal cortex

label_protocol: Bisulfite conversion was performed on 500 ng genomic DNA using the TrueMethyl Array kit (Cambridge Epigenetix). Oxidative bisulfite conversion was performed on 1 µg genomic DNA using the TrueMethyl Array kit (Cambridge Epigenetix). Briefly, denatured DNA underwent chemical oxidation followed by bisulfite conversion to specifically protect 5mC from deamination. While the recommended amount of 500 ng of DNA was sufficient for BS conversions, this was insufficient for oxBS analysis likely due to the additional harsh oxidation step. All conversion reactions were cleaned using SPRI-bead purification and eluted in 12 µl Tris buffer.

extract_protocol: DNA was isolated from enriched NeuN+ nuclei using the Qiagen QIAamp DNA Micro Kit (Cat. # 56304) according to manufacturer instructions, with the following modifications and optional steps to maximize yield. Given that samples were already homogenized during nuclei isolation, the sample lysis and incubation steps of the QIAamp DNA Micro Kit protocol were removed. Instead, 20 uL of proteinase K were added directly to each MACS eluate. Samples were then vortexed for 15 seconds and incubated at room temperature for 15 min. In addition, the optional carrier RNA was added to Buffer AL, the incubation time after the addition of 100% ethanol was increased to 10 min, the incubation time for the elution buffer was increased to 5 min, and the final elution step was repeated using 10 mM Tris-HCl pH 8.0.

value: parietal cortex

tag: disease state

value: PD

tag: race

value: White

value: Male

tag: age at death

tag: post-mortem interval (hours)


title: LLC tumor, CT-PAK2EC, 2

status: Public on Dec 10 2025

type: SRA

city: Montreal

first: Jean-Philippe

last: Gratton

address: 2900 Bd Edouard-Montpetit

country: Canada

institute: Université de Montréal

description:
Library name: CT-PAK2EC 2
Column name in counts_normalized_relative_to_library_size.xlsx: ct_ecpak2_2

library_source: transcriptomic

data_processing:
Tumors: Quality control of raw reads was assessed with FASTQC (v0.11.8), combined with MultiQC version 1.3. Reads were aligned to the GRCm38 genome using STAR (v2.5.1b), and raw counts were calculated with featureCounts (v1.6). DESeq2 (v1.24.0) was used to normalize gene readcounts.
HUVEC: Raw read quality was assessed with MultiQC (v1.11). Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic (v0.35) and aligned to the reference human genome version GRCh38 (gene annotation from Gencode v37, based on Ensembl 103) using STAR (v2.7.1a). Gene expressions were obtained from STAR both as readcounts and TPM values as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in FPKM and TPM values. DESeq2 (v1.30.1) was then used to normalize gene readcounts.
Assembly: GRCm38 and GRCh38
Supplementary files format and content: Excel file includes Deseq readcounts normalized to library for each Sample

molecule: total RNA

organism: Mus musculus

source_name: tumor

growth_protocol:
Lewis lung carcinoma (LLC) were cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100 ug/ml streptomycin. 1.5 x10^6 LLC cells were injected subcutaneously into the flank of 6- to 8-weeks old mice. The tumors grew for 18 days, after which tumors were harvested.
Human umbilical vein ECs (HUVECs) were cultured in M199 media supplemented with 20% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 0.05 mg/mL ECGS.

extract_protocol:
Total mRNA from tumors and HUVEC experiments was extracted using TRIzol Reagent, according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5 mg/21 days Tamoxifen slow-release pellets

tag: tissue

value: tumor

tag: cell line

value: LL/2 (LLC1)

tag: cell type

value: Lewis lung carcinoma

tag: genotype

value: CT

tag: treatment

value: Tamoxifen

tag: batch

value: RNAseq tumor


title: LLC tumor, KO-PAK2EC, 2

description:
Library name: KO-PAK2EC 2
Column name in counts_normalized_relative_to_library_size.xlsx: ko_ecpak2_2

value: PAK2 endothelial knockdown


title: IL-4 AMs

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

country: China

institute: Naval medical university

description: Library name: IL-4

library_source: genomic

data_processing:
Genome mapping was performed using Bowtie (version:0.12.8) and clean reads were compared to reference genome mm10. MACS (version 2.2.7.1) was applied to call peak.
The bam file and R package DiffBind were used to analyze the differences between the peaks of the specified two samples. The default parameter was set as fold change ≥ 2 or≤ 1/2 and P value < 0.05, and the differences between the obtained peakswere annotated.
The annotation program was the same as the above peak annotation program, including different peak location information, annotation information, etc.
Assembly: mm10
Supplementary files format and content: narrowPeak file that includes information of PHLPP1-binding DNA
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Mus musculus

growth_protocol: AMs were generated from bronchoalveolar lavage fluid (BALF)

extract_protocol:
CUT&Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions. Briefly, WT AMs were stimulated with IL-4 and then harvested after PBS wash. Cells (1 × 105) were bound with concanavalin A-coated magnetic beads and then incubated with antibodies against PHLPP1 (ProteinTech) at 4 °C overnight. On the next day, samples were incubated with a second antibody and then with Hyperactive pA/G-Transposon for 1 h. DNA was treated with TTBL at 37 °C for 1 h and extracted.
The librarys were constructed by purified DNA, and amplified using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions.

treatment_protocol: WT AMs were stimulated with IL-4 (20ng/ml) for 4 hours

value: Mus musculus

value: lung

value: AMs

value: Mouse primary alveolar macrophages


title: P453

status: Public on Dec 11 2025

type: genomic

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

institute: McGill University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: The R package minfi (v1.42.0) was used for preprocessing of IDAT files, quality control, and normalization in RStudio. Normalization was performed with noob using the preprocessNoob function in the minfi package. Two samples failed quality control due to elevated detection p-values (>0.01) and were excluded from further analyses, leaving a remaining total of 62 placenta samples.   A total of 865859 probes were detected on the Illumina 850K array. Unreliable probes (probes with elevated detection p-values >0.01, probes located on sex chromosomes, probes containing single nucleotide polymorphisms (SNPs) of minor allele frequency >1% within 5bp of the CpG site, and cross-reactive probes) were removed, leaving a total of 773321 filtered probes for downstream analyses. Additional normalization was performed with beta-mixture quantile normalization (BMIQ) using the ChAMP package (v2.26.0) in RStudio. Batch correction was also performed using the ChAMP package.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Placenta

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the QIAamp DNA Mini Kit (Qiagen cat. #51304) as per the manufacturer’s protocol.

treatment_protocol: The current study includes 64 placenta samples from the 3D Study, which were split evenly based on paternal age at conception: younger (n=21), middle (n=22) and older (n=21).

tag: paternal age group

value: Middle


title: P408

value: Old


title: Neuron_oxBS_99

country: USA

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 99-38

value: parietal cortex

tag: Sex

value: Female


title: UT AMs

description: Library name: UT

value: UT


title: 8-WUZHIFANG_(MoGene-1_0-st-v1)

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: NOD mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mouse submandibular gland

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Allogeneic BMSCs were originally isolated from the bone marrow of male BALB/c mice (6–8 weeks old) and were characterized for MSC surface markers. BMSCs at passage 3 (1*10^5 cells/mouse) were administered intravenously in 0.15 mL Phosphate-Buffered Saline (PBS) (20). Control animals received an equivalent volume of PBS intravenously.

value: submandibular glands

tag: age

value: 12 weeks

value: PBS


title: LLC tumor, KO-PAK2EC, 1

description:
Library name: KO-PAK2EC 1
Column name in counts_normalized_relative_to_library_size.xlsx: ko_ecpak2_1

value: tumor

value: LL/2 (LLC1)

value: Lewis lung carcinoma


title: 7-WUZHIFANG_(MoGene-1_0-st-v1)


title: 5-WUZHIFANG_(MoGene-1_0-st-v1)

value: BMSC


title: 4-WUZHIFANG_(MoGene-1_0-st-v1)


title: 2-WUZHIFANG_(MoGene-1_0-st-v1)


title: 1-WUZHIFANG_(MoGene-1_0-st-v1)


title: P446

value: Young


title: Neuron_oxBS_50

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-78

value: Control

value: White

value: Male


title: 9-WUZHIFANG_(MoGene-1_0-st-v1)


title: 3-WUZHIFANG_(MoGene-1_0-st-v1)


title: P484


title: Neuron_oxBS_98

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 19-02

value: PD


title: Neuron_oxBS_97

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-72


title: Neuron_oxBS_49

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-64

value: Unknown


title: Neuron_oxBS_48

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-17


title: Neuron_oxBS_92

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-27


title: Neuron_oxBS_93

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-30


title: Neuron_oxBS_95

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-39


title: Neuron_oxBS_46

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-37


title: Neuron_oxBS_45

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-19


title: Neuron_oxBS_89

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-05


title: Neuron_oxBS_47

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-50


title: Neuron_oxBS_96

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-65


title: Neuron_oxBS_91

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-14


title: Neuron_oxBS_87

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 16-23


title: Neuron_oxBS_42

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-78


title: Neuron_oxBS_86

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-69


title: Neuron_oxBS_43

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 16-10


title: P465

value: Old


title: Neuron_oxBS_44

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 16-32

value: parietal cortex


title: Neuron_oxBS_88

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-47


title: Neuron_oxBS_85

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-54


title: Neuron_oxBS_40

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-46

value: Female


title: P440

value: Middle


title: Neuron_oxBS_84

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-04


title: P487


title: 10-WUZHIFANG_(MoGene-1_0-st-v1)

value: submandibular glands


title: Neuron_oxBS_83

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 14-12


title: P437


title: Neuron_oxBS_90

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-12


title: P491


title: Neuron_oxBS_80

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-05


title: Neuron_oxBS_38

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-40


title: Neuron_oxBS_78

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-42


title: Neuron_oxBS_79

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-56


title: Neuron_oxBS_77

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-34


title: Neuron_oxBS_81

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-11


title: Neuron_oxBS_82

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-52


title: Neuron_oxBS_75

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 11-90


title: Neuron_oxBS_37

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-21


title: Neuron_oxBS_34

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-39


title: Neuron_oxBS_76

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-29


title: Neuron_oxBS_36

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-70


title: Neuron_oxBS_33

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-26


title: Neuron_oxBS_73

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 11-54


title: Neuron_oxBS_35

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-63


title: Neuron_oxBS_32

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-22


title: Neuron_oxBS_72

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-28


title: Neuron_oxBS_71

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-52


title: Neuron_oxBS_30

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-57


title: Neuron_oxBS_29

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-50


title: Neuron_oxBS_31

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-20


title: Neuron_oxBS_69

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-12


title: Neuron_oxBS_70

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-19


title: Neuron_oxBS_28

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-90


title: Neuron_oxBS_39

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-49


title: Neuron_oxBS_27

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-88


title: Neuron_oxBS_74

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 11-88


title: Neuron_oxBS_68

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-74


title: Neuron_oxBS_25

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-55


title: Neuron_oxBS_26

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-85


title: Neuron_oxBS_24

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-40


title: Neuron_oxBS_23

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-46


title: Neuron_oxBS_22

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-37


title: Neuron_oxBS_66

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-62


title: Neuron_oxBS_21

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-28


title: Neuron_oxBS_19

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-21


title: Neuron_oxBS_67

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-40


title: Neuron_oxBS_64

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-44


title: Neuron_oxBS_65

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-51


title: Neuron_oxBS_20

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-57


title: Neuron_oxBS_18

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-15


title: Neuron_oxBS_62

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-17


title: Neuron_oxBS_63

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-60


title: Neuron_oxBS_15

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 04-38


title: Neuron_oxBS_17

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-16


title: Neuron_oxBS_13

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-63


title: Neuron_oxBS_16

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-12


title: Neuron_oxBS_61

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 04-17


title: Neuron_oxBS_14

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 04-05


title: Neuron_oxBS_12

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-47


title: Neuron_oxBS_60

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-51


title: Neuron_oxBS_58

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-43


title: Neuron_oxBS_11

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-41


title: Neuron_oxBS_59

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-48


title: Neuron_oxBS_57

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-29


title: Neuron_oxBS_10

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-39


title: Neuron_oxBS_9

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-28


title: Neuron_oxBS_56

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-25


title: Neuron_oxBS_6

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-33


title: Neuron_oxBS_94

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-33


title: Neuron_oxBS_55

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-17


title: Neuron_oxBS_7

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-11


title: Neuron_oxBS_5

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-27


title: Neuron_oxBS_54

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-15


title: Neuron_oxBS_4

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-46


title: Neuron_oxBS_3

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-44


title: Neuron_oxBS_2

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-37


title: Neuron_oxBS_53

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 00-45


title: Neuron_oxBS_51

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 00-09


title: Neuron_oxBS_52

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 00-27


title: Neuron_BS_100

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 99-63


title: Neuron_bs_50

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-78


title: Neuron_BS_99

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 99-38


title: Neuron_oxBS_1

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-31


title: Neuron_BS_96

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-65


title: Neuron_BS_98

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 19-02


title: Neuron_BS_97

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-72


title: Neuron_bs_49

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-64


title: Neuron_BS_95

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-39


title: Neuron_BS_94

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-33


title: Neuron_BS_93

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-30


title: Neuron_BS_92

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-27


title: Neuron_BS_91

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-14


title: Neuron_BS_90

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-12


title: Neuron_BS_89

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-05


title: Neuron_oxBS_8

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-15


title: Neuron_bs_48

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 18-17


title: Neuron_BS_88

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-47


title: Neuron_bs_45

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-19


title: Neuron_bs_44

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 16-32


title: Neuron_bs_47

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-50


title: Neuron_BS_87

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 16-23


title: Neuron_bs_42

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-78


title: Neuron_bs_43

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 16-10


title: Neuron_BS_86

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-69


title: Neuron_BS_85

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-54


title: Neuron_bs_40

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-46


title: Neuron_BS_84

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-04


title: Neuron_BS_83

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 14-12


title: Neuron_BS_82

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-52


title: Neuron_BS_81

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-11


title: Neuron_bs_41

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-60


title: Neuron_bs_39

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-49


title: Neuron_BS_80

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-05


title: Neuron_BS_78

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-42


title: Neuron_bs_38

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 13-40


title: Neuron_BS_79

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-56


title: Neuron_BS_77

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-34


title: Neuron_BS_76

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-29


title: Neuron_bs_37

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 12-21


title: Neuron_BS_73

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 11-54


title: Neuron_BS_75

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 11-90


title: Neuron_bs_35

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-63


title: Neuron_bs_46

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 17-37


title: Neuron_bs_36

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-70


title: Neuron_bs_34

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-39


title: Neuron_BS_72

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-28


title: Neuron_bs_33

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-26


title: Neuron_bs_31

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-20


title: Neuron_bs_29

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-50


title: Neuron_bs_30

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-57


title: Neuron_bs_28

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-90


title: Neuron_BS_69

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-12


title: Neuron_BS_70

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-19


title: Neuron_BS_71

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 09-52


title: Neuron_bs_32

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 10-22


title: Neuron_bs_26

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-85


title: Neuron_BS_68

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-74


title: S. cerevisiae NTT1+, 5 mM ATP (rep3)

city: Charlottesville

first: Alaattin

last: Kaya

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description:
Library name: Sample 12
NTT1-expressing yeast treated with 5 mM ATP for 1 hour at mid-log phase; total RNA used for RNA-seq.

data_processing:
Raw reads were quality-checked and adapters removed. Clean paired-end reads were aligned to the S. cerevisiae reference genome (Ensembl R64-1-1) using HISAT2 v2.0.5. Gene counts were obtained with FeatureCounts v1.5.0. FPKM values were calculated using gene length and mapped read counts. Differential expression was performed with DESeq2 v1.20.0, and p-values adjusted using Benjamini–Hochberg FDR correction.
Assembly: Saccharomyces cerevisiae genome, Ensembl R64-1-1 (also equivalent to S288C reference genome)
Supplementary files format and content: Processed data include gene-level expression matrices. Files contain raw read counts generated with FeatureCounts and normalized expression values (FPKM). Each row represents a yeast gene (Ensembl R64-1-1 annotation), and each column corresponds to one RNA-seq sample.

organism: Saccharomyces cerevisiae

source_name: BY29034 background, QUEEN reporter

growth_protocol: Cells were cultured in complete synthetic medium (CSM) at 30°C with shaking (200–220 rpm) until mid-log phase (OD600 ~0.4–0.5).

extract_protocol:
Total RNA was extracted using the Quick-RNA Fungal/Bacterial MiniPrep Kit (Zymo Research) according to the manufacturer’s instructions.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Library Prep Kit following the manufacturer's instructions.

treatment_protocol: Cells were grown in complete synthetic medium (CSM) at 30°C to OD600 0.4–0.5 and treated with 5 mM extracellular ATP for 1 hour under shaking, as described in the RNA-seq methods. Untreated controls were processed in parallel.

value: BY29034 background, QUEEN reporter

value: PH-NTT1 integrated at genomic locus

value: 5 mM ATP, 1 hour


title: Neuron_bs_25

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-55


title: Neuron_bs_24

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-40


title: Neuron_bs_27

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 08-88


title: Neuron_bs_23

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-46


title: Neuron_BS_74

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 11-88


title: S. cerevisiae NTT1+, 5 mM ATP (rep2)

description:
Library name: Sample 11
NTT1-expressing yeast treated with 5 mM ATP for 1 hour at mid-log phase; total RNA used for RNA-seq.


title: S. cerevisiae NTT1+, 5 mM ATP (rep1)

description:
Library name: Sample 10
NTT1-expressing yeast treated with 5 mM ATP for 1 hour at mid-log phase; total RNA used for RNA-seq.


title: Neuron_BS_67

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-40


title: S. cerevisiae NTT1+, no ATP (rep3)

description:
Library name: Sample 9
NTT1-expressing yeast at mid-log phase, untreated; total RNA extracted for RNA-seq.


title: Neuron_bs_21

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-28


title: Neuron_bs_22

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 07-37


title: S. cerevisiae NTT1+, no ATP (rep2)

description:
Library name: Sample 8
NTT1-expressing yeast at mid-log phase, untreated; total RNA extracted for RNA-seq.


title: Neuron_BS_66

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-62


title: Neuron_bs_20

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-57


title: S. cerevisiae WT, 5 mM ATP (rep3)

description:
Library name: Sample 6
Wild-type yeast treated with 5 mM ATP for 1 hour at mid-log phase; total RNA used for RNA-seq.

value: wild-type (empty-vector control)


title: Neuron_BS_65

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-51


title: S. cerevisiae WT, 5 mM ATP (rep1)

description:
Library name: Sample 4
Wild-type yeast treated with 5 mM ATP for 1 hour at mid-log phase; total RNA used for RNA-seq.


title: Neuron_bs_19

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-21


title: Neuron_BS_64

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-44


title: S. cerevisiae WT, 5 mM ATP (rep2)

description:
Library name: Sample 5
Wild-type yeast treated with 5 mM ATP for 1 hour at mid-log phase; total RNA used for RNA-seq.


title: Neuron_oxBS_41

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 15-60


title: Neuron_BS_63

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-60


title: S. cerevisiae WT, no ATP (rep2)

description:
Library name: Sample 2
Wild-type yeast at mid-log phase, untreated; total RNA extracted for RNA-seq.


title: S. cerevisiae WT, no ATP (rep1)

description:
Library name: Sample 1
Wild-type yeast at mid-log phase, untreated; total RNA extracted for RNA-seq.


title: JejC WT rep 8

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

department: Pediatrics

institute: CWRU

description:
Library name: Sample 61
fpkm WT_JejC_7

data_processing:
Reads were trimmed and filtered using Trimmomatic (v 0.39), then aligned to UCSC mouse genome mm10 using Bowtie2 and Tophat (2.1.1). Assembly of transcriptomes and quantification was performed with Cufflinks (2.1.1). Expression levels are expressed as fragments per kilobase of exon per million fragments mapped (FPKM). Data was further analyzed and visualized using CummeRbund run under the R package (4.1.3). Statistical significance in differential gene expression between groups was assessed with Cuffdiff (2.1.1)
Hierarchical clustering of genes was generated using Complete Linkage as the clustering method, Euclidian distance as the similarity measure, and Z-Score as normalization with TIBCO Spotfire Software (Palo Alto, CA). Pathway analysis was performed using Gene Set Enrichment Analysis (GSEA) (Broad Institute, software.broadinstitute.org/gsea), a computational method that determines statistical significance of a priori defined set of genes between two groups and ClueGo within Cytoscape software v3.10.3 using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, WikiPathways (WP), Reactome pathways and Reactome reaction pathways, as well as GO biological process (GO BP).
Assembly: UCSC mm10
Supplementary files format and content: xlsx files contain FPKM values for each sample

source_name: Jejunum crypts

growth_protocol: RNA was extracted from 6-8 weeks old male mice, non-littermate wildtype (WT) and the previously established Cystic Fibrosis (CF) (G542X/G542X) mice on the C57Bl6/J background. Mice had unrestricted access to D12451i diet (research Diets, 45 kcal % fat) with acidifeid water

extract_protocol:
The small intestine was extracted in its entirety from stomach to cecum and flushed with cold phosphate buffered saline (PBS). Three-inch long intestinal segments were collected from the beginning, middle and end of the small intestine to correspond with duodenum, jejunum, and ileum respectively and frozen immediately in liquid nitrogen. The jejunum section was divided in half lengthwise prior to freezing, using one section for whole tissue RNA and the other for crypt isolation and subsequent RNA extraction. RNA was isolated using Rneasy mini kit (Qiagen), concentration and quality checked with the Nanodrop (ThermoScientific).
RNA-seq libraries were generated using TruSeq stranded Total RNA Ribo-Zero mouse gold kit (Illumina, San Diego, CA) and the quality of resulting libraries was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). Ileum (WT n=4, CF n=5) sequencing was carried out using an Illumina HiSeq 2500 Rapid Run flow cell – 2x100bp run. Duodenum (WT n=9, CF n=9), jejunum (WT n=8, CF n=9) and jejunum crypts (WT n=8, CF n=9) sequencing was carried out using an Illumina NextSeq 550 HO flowcell – 2x75bp run

value: Jejunum crypts

value: Wild type


title: Neuron_bs_17

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-16


title: Neuron_bs_18

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 06-15


title: Neuron_bs_15

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 04-38


title: JejC WT rep 5

description:
Library name: Sample 58
fpkm WT_JejC_4


title: JejC WT rep 3

description:
Library name: Sample 56
fpkm WT_JejC_2


title: Neuron_bs_14

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 04-05


title: S. cerevisiae NTT1+, no ATP (rep1)

description:
Library name: Sample 7
NTT1-expressing yeast at mid-log phase, untreated; total RNA extracted for RNA-seq.


title: Neuron_bs_13

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-63


title: JejC WT rep 2

description:
Library name: Sample 55
fpkm WT_JejC_1


title: Neuron_BS_61

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 04-17


title: Neuron_BS_60

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-51


title: JejC WT rep 1

description:
Library name: Sample 54
fpkm WT_JejC_0


title: JejC CF rep 9

description:
Library name: Sample 53
fpkm CF_JejC_8


title: Neuron_BS_59

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-48


title: S. cerevisiae WT, no ATP (rep3)

description:
Library name: Sample 3
Wild-type yeast at mid-log phase, untreated; total RNA extracted for RNA-seq.


title: JejC CF rep 7

description:
Library name: Sample 51
fpkm CF_JejC_6


title: Neuron_BS_58

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-43


title: Neuron_bs_11

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-41


title: Neuron_BS_62

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-17


title: JejC CF rep 5

description:
Library name: Sample 49
fpkm CF_JejC_4


title: JejC WT rep 6

description:
Library name: Sample 59
fpkm WT_JejC_5


title: JejC WT rep 7

description:
Library name: Sample 60
fpkm WT_JejC_6


title: Neuron_bs_16

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 05-12


title: JejC CF rep 3

description:
Library name: Sample 47
fpkm CF_JejC_2


title: JejC WT rep 4

description:
Library name: Sample 57
fpkm WT_JejC_3


title: Neuron_bs_8

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-15


title: Neuron_bs_9

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-28


title: Neuron_BS_56

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-25


title: JejC CF rep 1

description:
Library name: Sample 45
fpkm CF_JejC_0


title: JejC CF rep 2

description:
Library name: Sample 46
fpkm CF_JejC_1


title: Jej WT rep 7

description:
Library name: Sample 43
fpkm WT_Jej_6

source_name: Jejunum

value: Jejunum


title: Jej WT rep 8

description:
Library name: Sample 44
fpkm WT_Jej_7


title: Jej WT rep 6

description:
Library name: Sample 42
fpkm WT_Jej_5


title: Jej WT rep 5

description:
Library name: Sample 41
fpkm WT_Jej_4


title: JejC CF rep 8

description:
Library name: Sample 52
fpkm CF_JejC_7


title: Neuron_bs_5

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-27

value: Control


title: Neuron_bs_12

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-47

value: White


title: Jej WT rep 4

description:
Library name: Sample 40
fpkm WT_Jej_3


title: Neuron_bs_10

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-39

value: Male


title: JejC CF rep 6

description:
Library name: Sample 50
fpkm CF_JejC_5


title: Neuron_BS_54

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-15

value: PD


title: Neuron_bs_4

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-46


title: Neuron_BS_55

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-17


title: JejC CF rep 4

description:
Library name: Sample 48
fpkm CF_JejC_3


title: Jej WT rep 2

description:
Library name: Sample 38
fpkm WT_Jej_1


title: Jej WT rep 3

description:
Library name: Sample 39
fpkm WT_Jej_2


title: Jej CF rep9

description:
Library name: Sample 36
fpkm CF_Jej_8


title: Neuron_BS_57

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-29


title: Neuron_bs_1

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-31


title: Jej CF rep8

description:
Library name: Sample 35
fpkm CF_Jej_7


title: Neuron_bs_7

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 03-11


title: Neuron_bs_2

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-37


title: Jej WT rep 1

description:
Library name: Sample 37
fpkm WT_Jej_0


title: Neuron_bs_3

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 01-44


title: Neuron_bs_6

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 02-33


title: Neuron_BS_52

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 00-27


title: Neuron_BS_53

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 00-45


title: Jej CF rep6

description:
Library name: Sample 33
fpkm CF_Jej_5


title: Jej CF rep7

description:
Library name: Sample 34
fpkm CF_Jej_6


title: Neuron_BS_51

description: NeuN-positive (NeuN+) nuclei enriched from 100 mg of flash frozen parietal cortex tissue taken from subject 00-09


title: Jej CF rep5

description:
Library name: Sample 32
fpkm CF_Jej_4


title: MDA-MB-231-TRAIL-6h-trt3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

institute: UNIVERSITY OF FLORIDA

description: Library name: T6-3

data_processing:
Reads acquired from the Illumina Novaseq 6000 platform were cleaned up with the cutadapt program (version 3.4) to trim off sequencing adaptors and low-quality bases
The cleaned reads were mapped to the reference sequences (mm10 and GRCh38)  using the read mapper of the STAR package (Spliced Transcripts Alignment to a Reference, v2.7.9a). The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v2.03), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates and count uniquely mapped reads for gene expression analysis
Assembly: Homo sapiens and GRCh38
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

growth_protocol: MDA-MB-231 cells were cultured and maintained in Dulbecco's modified Eagle medium (DMEM, Invitrogen) supplemented with 10% fetal bovine serum (FBS; HyClone, Logan, UT) and 1% antibiotic–antimycotic (Invitrogen) at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted after 12h using RNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Illumina RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF).

treatment_protocol: 150 000 cells of MDA-MB-231 were seeded in a 12-well plate, incubated 24 h before treatment with grassystatin G (40 uM), TRAIL (25 ng mL−1), the combination of both, and solvent control in triplicates. RNA was extracted after treatments of 6 h and 12 h using RNeasy Mini Kit (Qiagen). RNA-seq was done by the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF). Illumina RNA library construction and subsequent NextSeq500 sequencing (Illumina) were done as described.

value: Epithelial cell

value: WT; triple-negative breast cancer cell line; aneuploid

value: TRAIL

tag: time point


title: Jej CF rep2

description:
Library name: Sample 29
fpkm CF_Jej_1


title: Jej CF rep3

description:
Library name: Sample 30
fpkm CF_Jej_2


title: MDA-MB-231-TRAIL-6h-trt2

description: Library name: T6-2


title: Jej CF rep4

description:
Library name: Sample 31
fpkm CF_Jej_3


title: MDA-MB-231-TRAIL-3h-trt2

description: Library name: T3-2


title: MDA-MB-231-TRAIL-3h-trt3

description: Library name: T3-3


title: MDA-MB-231-TRAIL-3h-trt1

description: Library name: T3-1


title: Duo WT rep 8

description:
Library name: Sample 17
fpkm WT_Duo_M_7

source_name: Duodenum

value: Duodenum


title: MDA-MB-231-TRAIL-12h-trt3

description: Library name: T12-3


title: Jej CF rep1

description:
Library name: Sample 28
fpkm CF_Jej_0


title: Duo WT rep 9

description:
Library name: Sample 18
fpkm WT_Duo_M_8


title: Duo WT rep 6

description:
Library name: Sample 15
fpkm WT_Duo_M_5


title: Duo WT rep 7

description:
Library name: Sample 16
fpkm WT_Duo_M_6


title: MDA-MB-231-TRAIL-12h-trt2

description: Library name: T12-2


title: MDA-MB-231-G-6h-trt3

description: Library name: g6-3

value: Grassystatin G


title: Duo WT rep 5

description:
Library name: Sample 14
fpkm WT_Duo_M_4


title: Duo WT rep 4

description:
Library name: Sample 13
fpkm WT_Duo_M_3


title: MDA-MB-231-G-6h-trt1

description: Library name: g6-1


title: MDA-MB-231-TRAIL-12h-trt1

description: Library name: T12-1


title: Duo WT rep 2

description:
Library name: Sample 11
fpkm WT_Duo_M_1


title: Duo WT rep 3

description:
Library name: Sample 12
fpkm WT_Duo_M_2


title: MDA-MB-231-G-3h-trt3

description: Library name: g3-3


title: MDA-MB-231-G-3h-trt2

description: Library name: g3-2


title: MDA-MB-231-G-6h-trt2

description: Library name: g6-2


title: Duo CF rep 8

description:
Library name: Sample 8
fpkm CGX_Duo_M_7


title: MDA-MB-231-G-3h-trt1

description: Library name: g3-1


title: MDA-MB-231-TRAIL-6h-trt1

description: Library name: T6-1


title: MDA-MB-231-G-12h-trt3

description: Library name: g12-3


title: Duo CF rep 7

description:
Library name: Sample 7
fpkm CGX_Duo_M_6


title: MDA-MB-231-G-12h-trt1

description: Library name: g12-1


title: Duo CF rep 6

description:
Library name: Sample 6
fpkm CGX_Duo_M_5


title: MDA-MB-231-G-12h-trt2

description: Library name: g12-2


title: Duo CF rep 5

description:
Library name: Sample 5
fpkm CGX_Duo_M_4


title: MDA-MB-231-com-6h-ctr3

description: Library name: CO6-3

value: Combo (grassystatin G+TRAIL)


title: Duo CF rep 3

description:
Library name: Sample 3
fpkm CGX_Duo_M_2


title: MDA-MB-231-com-3h-ctr3

description: Library name: CO3-3


title: MDA-MB-231-com-6h-ctr2

description: Library name: CO6-2


title: MDA-MB-231-com-6h-ctr1

description: Library name: CO6-1


title: Duo CF rep 1

description:
Library name: Sample 1
fpkm CGX_Duo_M_0


title: Duo CF rep 4

description:
Library name: Sample 4
fpkm CGX_Duo_M_3


title: Duo CF rep 9

description:
Library name: Sample 9
fpkm CGX_Duo_M_8


title: MDA-MB-231-com-3h-ctr1

description: Library name: CO3-1


title: loratadine and oxacillin biol rep F

city: High Point

first: Heather

middle: Bennett

last: Miller

state: NC

address: One University Parkway

department: Chemistry

institute: High Point University

description: Library name: VloroxF

data_processing:
Quality control of resulting reads included removing adapter-containing reads, removing reads where “N” was > 10%, and removing low-quality reads where the quality value of over 50% of the bases was ≤ 5.
The remaining reads were mapped to the reference genome with GenBank accession number AHBK00000000.1 using Bowtie2.
Gene expression levels were quantified as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) and averaged among biological triplicate samples.
Assembly: Staphylococcus aureus subsp. Aureus VRS1 GenBank AHBK00000000.1  https://www.ncbi.nlm.nih.gov/nuccore/387723839
Supplementary files format and content: An Excel spreadsheet for all treatment comparison groups that contain all analyzed replicates, gene information, read counts, fpkm, log2fold change and adjusted pvalues

organism: Staphylococcus aureus

source_name: bacterial cells

growth_protocol: S. aureus VRSA-1 was purchased from the American Type Culture Collection. Cultures were grown overnight in CAMHB at 37 °C with shaking. Mid-log-phase cultures were diluted to 5 × 105 CFU mL–1 in CAMHB.

extract_protocol:
Total RNA was purified from 3mL of culture using a Qiagen RNeasy kit and Thermo's Turbo DNase kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cell suspension (3 mL) was aliquoted into sterile culture tubes, and compound 8 was added to a final concentration of 25uM, loratadine to 50uM, oxacillin to 4ug/mL, vancomycin to 16ug/mL. Untreated cultures served as negative controls. These treatments continued for 1 hour while in the shaking incubator.

value: bacterial cells

value: bacterial

value: cotreated w/oxacillin and loratadine


title: compound 8 and oxacillin biol rep F

description: Library name: V8oxF

value: cotreated w/oxacillin and compound 8


title: compound 8 and vancomycin biol rep F

description: Library name: V8vanF

value: cotreated w/vancomycin and compound 8


title: Duo WT rep 1

description:
Library name: Sample 10
fpkm WT_Duo_M_0

value: Wild type


title: MDA-MB-231-6h-ctr3

description: Library name: C6-3


title: vancomycin biol rep F

description: Library name: VvanF

value: vancomycin treated, 16 ug/mL


title: MDA-MB-231-6h-ctr2

description: Library name: C6-2

value: Control


title: MDA-MB-231-com-12h-ctr2

description: Library name: CO12-2


title: loratadine and vancomycin biol rep F

description: Library name: VlorvanF

value: cotreated w/vancomycin and loratadine


title: loratadine biol rep F

description: Library name: VlorF

value: loratadine treated, 50 uM


title: oxacillin biol rep F

description: Library name: VoxF

value: oxacillin treated, 4 ug/mL


title: MDA-MB-231-6h-ctr1

description: Library name: C6-1

value: Epithelial cell


title: untreated biol rep F

description: Library name: VunF

value: untreated, DMSO only


title: MDA-MB-231-3h-ctr3

description: Library name: C3-3

value: WT; triple-negative breast cancer cell line; aneuploid


title: compound 8 biol rep F

description: Library name: V8F

value: compound 8 treated, 25uM


title: Duo CF rep 2

description:
Library name: Sample 2
fpkm CGX_Duo_M_1

value: Duodenum


title: MDA-MB-231-com-3h-ctr2

description: Library name: CO3-2

value: Combo (grassystatin G+TRAIL)


title: MDA-MB-231-3h-ctr1

description: Library name: C3-1


title: MDA-MB-231-3h-ctr2

description: Library name: C3-2


title: MDA-MB-231-12h-ctr3

description: Library name: C12-3


title: loratadine and oxacillin biol rep E

description: Library name: VloroxE

value: bacterial cells


title: compound 8 and vancomycin biol rep E

description: Library name: V8vanE

value: bacterial


title: loratadine and vancomycin biol rep E

description: Library name: VlorvanE


title: MDA-MB-231-12h-ctr2

description: Library name: C12-2


title: MDA-MB-231-com-12h-ctr3

description: Library name: CO12-3


title: compound 8 and oxacillin biol rep E

description: Library name: V8oxE


title: MDA-MB-231-com-12h-ctr1

description: Library name: CO12-1


title: MDA-MB-231-12h-ctr1

description: Library name: C12-1


title: vancomycin biol rep E

description: Library name: VvanE


title: compound 8 biol rep E

description: Library name: V8E


title: PRG Day 14 autologous PBMC culture replicate 2

city: Toulouse

first: Vera

last: Pancaldi

address: 2 Avenue Hubert Curien

country: France

institute: Toulouse Cancer Research Center (CRCT)

description:
Library name: B8
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 14, replicate 2.

data_processing:
Base calling was performed on the Illumina NovaSeq 6000 using NovaSeq Control Software. BCL files were converted to fastq.gz using Illumina BCL Convert v4.0.3 with the run-specific SampleSheet. fastq.gz files were produced per lane (L001, L002) and per read (R1, R2).
Quality control of raw reads was performed using fastq.gzC v0.11.9, and summary reports were aggregated with MultiQC. fastq.gz files from different lanes were merged using `cat` to obtain one R1 and one R2 file per sample. Adapter and quality trimming were done using Cutadapt (`cutadapt -q 15,10`) on paired-end reads.
The human genome (GRCh38/hg38) was indexed from Ensembl release 106 FASTA and GTF files. Trimmed reads were aligned using STAR v2.7 with parameters: `--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode TranscriptomeSAM --alignSoftClipAtReferenceEnds No --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate`
Transcript-level and gene-level quantification was performed with RSEM v1.3. RSEM reference files were generated using `rsem-prepare-reference` from the same genome and annotation. Expression estimates for each sample were computed from STAR’s `Aligned.toTranscriptome.out.bam` files using `rsem-calculate-expression` with paired-end mode.
Gene count matrices were produced using `rsem-generate-data-matrix` from all sample `.genes.results` files. The processed data submitted to GEO correspond to raw gene counts per gene per sample, provided in tab-delimited format.
Assembly: GRCh38 (hg38), Ensembl annotation release 106
Supplementary files format and content: Processed data files are tab-delimited text matrices containing raw gene-level counts. Rows correspond to Ensembl gene IDs with gene symbols, and columns correspond to individual samples. Values represent RSEM expected counts generated after alignment with STAR and quantification with RSEM. TPM values were generated for downstream analyses but are not included in the GEO submission.

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from CLL patient blood by Ficoll density gradient centrifugation. Autologous cultures consisted of whole PBMCs; monocultures consisted of purified CLL B cells obtained via negative selection. Cells were cultured in RPMI-1640 GlutaMax supplemented with 10% FBS and 1% penicillin–streptomycin at 37°C, 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following manufacturer instructions. RNA quality and quantity were assessed prior to library preparation.
Stranded mRNA-seq libraries were prepared using the Illumina Stranded mRNA Prep kit (poly-A mRNA enrichment) with IDT for Illumina Unique Dual (UD) Indexes. Libraries were prepared following the manufacturer’s recommended protocol, pooled, and sequenced on an Illumina NovaSeq 6000 S1 flow cell using a paired-end 2 × 75 bp configuration.

treatment_protocol: Non-adherent cells were collected at days 1, 4, 8, 11 and 14 for RNA extraction. No additional stimulation was applied.

value: Blood

value: Primary cells

value: Peripheral blood mononuclear cells (PBMC) from CLL patient

value: autologous PBMC culture


title: PRG Day 14 autologous PBMC culture replicate 1

description:
Library name: A8
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 14, replicate 1.


title: oxacillin biol rep E

description: Library name: VoxE


title: PRG Day 11 CLL B-cell monoculture replicate 2

description:
Library name: H7
PRG patient CLL sample, purified CLL B-cell monoculture, Day 11, replicate 2.

value: Chronic lymphocytic leukaemia B cells

value: CLL B-cell monoculture


title: untreated biol rep E

description: Library name: VunE


title: loratadine biol rep E

description: Library name: VlorE


title: PRG Day 11 CLL B-cell monoculture replicate 1

description:
Library name: G7
PRG patient CLL sample, purified CLL B-cell monoculture, Day 11, replicate 1.


title: PRG Day 11 autologous PBMC culture replicate 2

description:
Library name: F7
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 11, replicate 2.


title: compound 8 and vancomycin biol rep D

description: Library name: V8vanD

value: cotreated w/vancomycin and compound 8


title: vancomycin biol rep D

description: Library name: VvanD

value: vancomycin treated, 16 ug/mL


title: loratadine and oxacillin biol rep D

description: Library name: VloroxD

value: cotreated w/oxacillin and loratadine


title: compound 8 and oxacillin biol rep D

description: Library name: V8ox

value: cotreated w/oxacillin and compound 8


title: PRG Day 14 CLL B-cell monoculture replicate 1

description:
Library name: C8
PRG patient CLL sample, purified CLL B-cell monoculture, Day 14, replicate 1.


title: PRG Day 8 CLL B-cell monoculture replicate 2

description:
Library name: D7
PRG patient CLL sample, purified CLL B-cell monoculture, Day 8, replicate 2.


title: PRG Day 8 CLL B-cell monoculture replicate 1

description:
Library name: C7
PRG patient CLL sample, purified CLL B-cell monoculture, Day 8, replicate 1.


title: oxacillin biol rep D

description: Library name: VoxD

value: oxacillin treated, 4 ug/mL


title: PRG Day 8 autologous PBMC culture replicate 2

description:
Library name: B7
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 8, replicate 2.


title: PRG Day 14 CLL B-cell monoculture replicate 2

description:
Library name: D8
PRG patient CLL sample, purified CLL B-cell monoculture, Day 14, replicate 2.


title: loratadine biol rep D

description: Library name: VlorD

value: loratadine treated, 50 uM


title: untreated biol rep D

description: Library name: VunD

value: untreated, DMSO only


title: PRG Day 4 CLL B-cell monoculture replicate 1

description:
Library name: G6
PRG patient CLL sample, purified CLL B-cell monoculture, Day 4, replicate 1.


title: PRG Day 8 autologous PBMC culture replicate 1

description:
Library name: A7
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 8, replicate 1.


title: PRG Day 4 autologous PBMC culture replicate 2

description:
Library name: F6
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 4, replicate 2.


title: PRG Day 4 CLL B-cell monoculture replicate 2

description:
Library name: H6
PRG patient CLL sample, purified CLL B-cell monoculture, Day 4, replicate 2.


title: PRG Day 4 autologous PBMC culture replicate 1

description:
Library name: E6
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 4, replicate 1.


title: PRG Day 1 CLL B-cell monoculture replicate 1

description:
Library name: C6
PRG patient CLL sample, purified CLL B-cell monoculture, Day 1, replicate 1.


title: PRG Day 1 autologous PBMC culture replicate 2

description:
Library name: B6
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 1, replicate 2.


title: SAS Day 14 CLL B-cell monoculture replicate 1

description:
Library name: G5
SAS patient CLL sample, purified CLL B-cell monoculture, Day 14, replicate 1.


title: SAS Day 14 CLL B-cell monoculture replicate 2

description:
Library name: H5
SAS patient CLL sample, purified CLL B-cell monoculture, Day 14, replicate 2.


title: PRG Day 1 autologous PBMC culture replicate 1

description:
Library name: A6
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 1, replicate 1.


title: SAS Day 14 autologous PBMC culture replicate 2

description:
Library name: F5
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 14, replicate 2.


title: SAS Day 14 autologous PBMC culture replicate 1

description:
Library name: E5
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 14, replicate 1.


title: SAS Day 11 CLL B-cell monoculture replicate 2

description:
Library name: D5
SAS patient CLL sample, purified CLL B-cell monoculture, Day 11, replicate 2.


title: SAS Day 11 CLL B-cell monoculture replicate 1

description:
Library name: C5
SAS patient CLL sample, purified CLL B-cell monoculture, Day 11, replicate 1.


title: Arabidopsis vtc3-2

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

country: Japan

institute: Shimane University

description:
Library name: Sample 8
Column name in All_processed_data.csv: vtc3-2

data_processing:
Sequencing was performed using an Illumina MiSeq with the MiSeq Reagent Kit v3 (300 cycles; Illumina). RNA-seq data were obtained from triplicate biological samples (n = 3 per group) and statistically analyzed. Read mapping, data processing, and statistical analyses were conducted using the CLC Genomics Workbench (version 9.5.2).
Assembly: not applicapable
Supplementary files format and content: An excel file (All_processed_data.csv) showing read counts and RPKM

organism: Arabidopsis thaliana

source_name: Shoots

growth_protocol: Arabidopsis wild-type and mutant plants were cultivated on half-strength Murashige and Skoog (MS) medium supplemented with 1% sucrose under a 16-hour photoperiod at 100 µmol photons m-2 s-1 and 22°C, with an 8-hour dark period at 20°C (LH-240S, NK System) for two weeks.

extract_protocol:
Total RNA was extracted from shoot tissues using RNAiso Plus (Takara, Japan) and purified with NucleoSpin RNA Plus (Takara).
RNA was fragmented and converted to double-stranded DNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina). Library quality and quantity were assessed using a Bioanalyzer (Agilent) and a KAPA Library Quantification Kit (KAPA Biosystems), respectively.

treatment_protocol: Two-week-old wild-type, vtc2-4, and vtc3-3 seedlings, grown on half-strength MS medium supplemented with 1% sucrose under the same conditions described above, were incubated in darkness for two days, followed by a six-hour exposure to growth light (100 µmol photons m-2 s-1).

value: Shoots

value: Light exposure (6 h)


title: Arabidopsis vtc3-3

description:
Library name: Sample 9
Column name in All_processed_data.csv: vtc3-3


title: SAS Day 11 autologous PBMC culture replicate 2

description:
Library name: B5
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 11, replicate 2.


title: Arabidopsis vtc3-1

description:
Library name: Sample 7
Column name in All_processed_data.csv: vtc3-1


title: PRG Day 11 autologous PBMC culture replicate 1

description:
Library name: E7
PRG patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 11, replicate 1.


title: MSC bone marrow_OA_rep2

city: Berlin

first: Julia

last: Sonnleitner

address: Charitéplatz 1

country: Germany

institute: Charité - Universitaetsmedizin Berlin

description: Gene expression data from MSCs from OA compared to non-OA donors

hyb_protocol: 15 μg of fragmented cRNA was hybridized to gene chips for 16 h at 45°C. Gene chips were washed and stained as recommended. (Affymetrix)

scan_protocol: Chips were scanned with the GeneArray scanner controlled by Affymetrix GCOS 1.4 software (Affymetrix).

data_processing: Raw gene expression data were processed and normalized with the GCOS 1.4 software (Affymetrix).

source_name: OA donor

label_protocol: 200 ng of total RNA was used to synthesize biotin-labeled cRNA.

growth_protocol: OA MSCs were isolated as previously described from cancellous bone of femoral heads from patients undergoing hip replacement due to osteoarthritis. Non-OA MSCs (ND) gained from human bone marrow that was harvested by aspiration of the iliac crest of patients for diagnostic reasons or due to fractures. Primary cells were cultured at 37 °C and 5% CO2; medium was changed every 2 to 3 days. As cell culture medium we used Dulbecco’s Modified Eagle Medium (DMEM 1 g/l glucose; Biochrom, Schaffhausen, Switzerland) supplemented with 10% fetal bovine serum (FBS; HyClone, Cramlington, UK), 20 mM HEPES (Biochrom), 2 mM L-glutamine (Biochrom), 1% penicillin (100 units/ml)/streptomycin (100 μg/ml) (Sigma-Aldrich, St. Louis, MO, USA) and 2 ng/ml human basic-fibroblast growth factor (bFGF; Pepro Tech, London, UK). Monolayer MSCs were detached with 0.05% trypsin/EDTA (Biochrom) at 90% confluency and reseeded at 5 x 103 cells/cm2. Cells in passage 2 were used for the subsequent analysis.

extract_protocol: Subsequently, cells were lysed with Tri®Reagent (Sigma-Aldrich). For phase separation, 1-bromo-3-chloropropane  (Sigma-Aldrich) was added to samples. Afte centrifugation, the upper phase was transferred and mixed with 70% ethanol (1:1 v/v). Total cellular RNA isolation was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. Prior to further processing of total RNA for microarray analysis, RNA integrity was assessed using the Agilent RNA 6,000 Nano Kit according to the manufacturer's protocol with the 2,100 Bioanalyzer (Agilent Technologies).

treatment_protocol: No treatment was administered.

value: bone marrow


title: MSC bone marrow_OA_rep3


title: MSC bone marrow_ND_rep3

source_name: non-OA donor


title: PRG Day 1 CLL B-cell monoculture replicate 2

description:
Library name: D6
PRG patient CLL sample, purified CLL B-cell monoculture, Day 1, replicate 2.


title: MSC bone marrow_ND_rep1


title: MSC bone marrow_OA_1000 nM CCL25_biological rep2

source_name: MSCs derived from bone marrow of OA patients, treated with 1000 nM CCL25

growth_protocol: OA MSCs were isolated as previously described from cancellous bone of femoral heads from patients undergoing hip replacement due to osteoarthritis. Primary cells were cultured at 37 °C and 5% CO2; medium was changed every 2 to 3 days. As cell culture medium we used Dulbecco’s Modified Eagle Medium (DMEM 1 g/l glucose; Biochrom, Schaffhausen, Switzerland) supplemented with 10% fetal bovine serum (FBS; HyClone, Cramlington, UK), 20 mM HEPES (Biochrom), 2 mM L-glutamine (Biochrom), 1% penicillin (100 units/ml)/streptomycin (100 μg/ml) (Sigma-Aldrich, St. Louis, MO, USA) and 2 ng/ml human basic-fibroblast growth factor (bFGF; Pepro Tech, London, UK). Monolayer MSCs were detached with 0.05% trypsin/EDTA (Biochrom) at 90% confluency and reseeded at 5 x 103 cells/cm2.

extract_protocol: Cells were lysed with Tri®Reagent (Sigma-Aldrich). For phase separation, 1-bromo-3-chloropropane  (Sigma-Aldrich) was added to samples. Afte centrifugation, the upper phase was transferred and mixed with 70% ethanol (1:1 v/v). Total cellular RNA isolation was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. Prior to further processing of total RNA for microarray analysis, RNA integrity was assessed using the Agilent RNA 6,000 Nano Kit according to the manufacturer's protocol with the 2,100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were detached at the end of passage 3, 6 x 105 cells were seeded in 25 cm² flasks and stimulated with 1,000 nM CCL25 in deprivation medium for 20 hours at 37 °C and 5% CO2. Controls were incubated in deprivation medium only.

value: treated with 1000 nM CCL25 in deprivation medium.


title: MSC bone marrow_ND_rep2


title: MSC bone marrow_OA_1000 nM CCL25_biological rep1


title: SAS Day 11 autologous PBMC culture replicate 1

description:
Library name: A5
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 11, replicate 1.

value: Blood


title: MSC bone marrow_OA_1000 nM CCL25_biological rep3


title: Arabidopsis vtc2-2

description:
Library name: Sample 5
Column name in All_processed_data.csv: vtc2-2


title: MSC bone marrow_OA_rep1


title: SAS Day 8 CLL B-cell monoculture replicate 2

description:
Library name: H4
SAS patient CLL sample, purified CLL B-cell monoculture, Day 8, replicate 2.

value: Primary cells


title: Arabidopsis vtc2-1

description:
Library name: Sample 4
Column name in All_processed_data.csv: vtc2-1


title: Arabidopsis WT-3

description:
Library name: Sample 3
Column name in All_processed_data.csv: WT-3

value: wild type


title: MSC bone marrow_OA_0 nM CCL25_biological rep2

source_name: MSCs derived from bone marrow of OA patients, without 1000 nM CCL25

value: treated with deprivation medium only


title: SAS Day 8 autologous PBMC culture replicate 2

description:
Library name: F4
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 8, replicate 2.

value: Peripheral blood mononuclear cells (PBMC) from CLL patient

value: autologous PBMC culture


title: Arabidopsis WT-2

description:
Library name: Sample 2
Column name in All_processed_data.csv: WT-2


title: Arabidopsis WT-1

description:
Library name: Sample 1
Column name in All_processed_data.csv: WT-1


title: SAS Day 8 autologous PBMC culture replicate 1

description:
Library name: E4
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 8, replicate 1.


title: SAS Day 4 CLL B-cell monoculture replicate 2

description:
Library name: D4
SAS patient CLL sample, purified CLL B-cell monoculture, Day 4, replicate 2.

value: Chronic lymphocytic leukaemia B cells

value: CLL B-cell monoculture


title: MSC bone marrow_OA_0 nM CCL25_biological rep1


title: Arabidopsis vtc2-3

description:
Library name: Sample 6
Column name in All_processed_data.csv: vtc2-3


title: MSC bone marrow_OA_0 nM CCL25_biological rep3


title: SAS Day 4 autologous PBMC culture replicate 2

description:
Library name: B4
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 4, replicate 2.


title: SAS Day 4 autologous PBMC culture replicate 1

description:
Library name: A4
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 4, replicate 1.


title: SAS Day 1 CLL B-cell monoculture replicate 2

description:
Library name: H3
SAS patient CLL sample, purified CLL B-cell monoculture, Day 1, replicate 2.


title: SAS Day 4 CLL B-cell monoculture replicate 1

description:
Library name: C4
SAS patient CLL sample, purified CLL B-cell monoculture, Day 4, replicate 1.


title: MR71

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Library name: Sample 156

data_processing:
De-multiplexing and generation of FASTQ files were performed using Illumina CASAVA v1.8.2.
FastQC v0.11.7 (RRID: SCR_014583) was used to examine the quality of raw reads and cutadapt v1.18 was used for trimming the sequencing adaptors (5’- AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’, -trim-n). Reads unlikely to be properly sequenced mature miRNA transcripts were discarded (reads shorter than 16 nt or longer than 25 nt with –m 16 –M 25 in cutadapt).
Alignment and quantification of mature miRNAs based on miRBase v22 (RRID: SCR_003152) were performed with miRDeep2 v0.1.0 with mapper.pl parameters –e –h –m –i –j and quantifier.pl parameter –k –j –d -P. For mature miRNAs associated with multiple precursor miRNAs, the max counts were used.
We performed miRNA-seq sample quality assessments and miRNA filtering separately for each sample type (endobronchial biopsies and bronchial brushes). We limited the analysis to the miRNA samples with previously analyzed (GSE109743, dbGaP:phs003185.v1.p1) matched mRNA expression profiles (n=160 biopsies, n=89 brushes). The raw counts were converted into log2 counts per million of miRNA reads mapped (logCPM) and quantile normalized with voom. miRNAs with logCPM less than 1 in more than half of the samples were removed. We excluded samples (n=4 biopsies, n=2 brushes) if sequencing quality metrics were outside 2 standard deviations from the mean. The quality metrics we used included the first and the second principal components from the PCA using filtered miRNA expression, the mean Pearson expression correlation with all other samples across the filtered miRNAs, and the transcript integrity number (TIN) of the matched mRNA sequencing sample (calculated using RSeQC v3.0.0, RRID: SCR_005275). Finally, 156 biopsies and 87 brush samples from 30 patients were retained.
The gene filter and normalization described above were performed on the final high-quality samples with matching mRNA data (n=525 miRNAs in biopsies and n=489 miRNAs in brushes). The residual miRNA expressions adjusting for sequencing batch were computed with limma (RRID: SCR_010943) for downstream analysis.
Assembly: hg38
Supplementary files format and content: PCGA_miRNA_raw_count_table_BX.csv: Comma-separated value (CSV) table of raw counts, 2656 miRNAs x 156 samples
Supplementary files format and content: PCGA_miRNA_residual_table_BX.csv: Comma-separated value (CSV) table of residuals, 525 rows x 156 columns

source_name: bronchial biopsy

extract_protocol:
miRNA was extracted from biopsies or brushing samples using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
miRNA sequencing libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEBioLabs). Sequencing adapters that target the 3’ hydroxyl group of small RNAs were ligated and the transcripts were reverse transcribed and PCR-amplified into single-stranded cDNA libraries. The libraries were pooled, and size selected for small RNA fragments on PAGE gel in groups of 6-10.

value: bronchial biopsy

tag: pcga id

tag: patient id

tag: flowcell

tag: dysplasia grade

value: unknown

tag: molecular subtype

value: Secretory

tag: progression status

tag: median tin


title: MR2R-18

description: Library name: Sample 153

tag: tissue

value: hyperplasia

value: Proliferative

value: normal/stable


title: MR_266

description: Library name: Sample 154

value: Inflammatory


title: MR2R-17

description: Library name: Sample 155


title: MR267

description: Library name: Sample 152

value: metaplasia


title: SAS Day 8 CLL B-cell monoculture replicate 1

description:
Library name: G4
SAS patient CLL sample, purified CLL B-cell monoculture, Day 8, replicate 1.

tag: cell line


title: SAS Day 1 CLL B-cell monoculture replicate 1

description:
Library name: G3
SAS patient CLL sample, purified CLL B-cell monoculture, Day 1, replicate 1.

tag: cell type


title: SAS Day 1 autologous PBMC culture replicate 2

description:
Library name: F3
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 1, replicate 2.


title: MR2R-20

description: Library name: Sample 150

value: mild dysplasia

value: progressive/persistent


title: SAS Day 1 autologous PBMC culture replicate 1

description:
Library name: E3
SAS patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 1, replicate 1.

value: Blood

value: Primary cells


title: 666-MR201

description: Library name: Sample 148


title: MR200

description: Library name: Sample 151

value: moderate dysplasia

value: regressive


title: MR268

description: Library name: Sample 149


title: MR160

description: Library name: Sample 147


title: MR2R-19

description: Library name: Sample 146


title: DAR Day 14 CLL B-cell monoculture replicate 1

description:
Library name: C3
DAR patient CLL sample, purified CLL B-cell monoculture, Day 14, replicate 1.


title: DAR Day 14 autologous PBMC culture replicate 2

description:
Library name: B3
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 14, replicate 2.

value: Peripheral blood mononuclear cells (PBMC) from CLL patient

value: autologous PBMC culture


title: DAR Day 14 autologous PBMC culture replicate 1

description:
Library name: A3
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 14, replicate 1.


title: MR199

description: Library name: Sample 145

value: Normal


title: DAR Day 14 CLL B-cell monoculture replicate 2

description:
Library name: D3
DAR patient CLL sample, purified CLL B-cell monoculture, Day 14, replicate 2.

value: Chronic lymphocytic leukaemia B cells

value: CLL B-cell monoculture


title: DAR Day 11 CLL B-cell monoculture replicate 1

description:
Library name: G2
DAR patient CLL sample, purified CLL B-cell monoculture, Day 11, replicate 1.


title: MR_159

description: Library name: Sample 144

value: bronchial biopsy


title: DAR Day 11 autologous PBMC culture replicate 2

description:
Library name: F2
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 11, replicate 2.


title: MR_106

description: Library name: Sample 143

value: unknown


title: MR242

description: Library name: Sample 142

value: Proliferative


title: DAR Day 11 autologous PBMC culture replicate 1

description:
Library name: E2
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 11, replicate 1.


title: DAR Day 11 CLL B-cell monoculture replicate 2

description:
Library name: H2
DAR patient CLL sample, purified CLL B-cell monoculture, Day 11, replicate 2.


title: MR_239

description: Library name: Sample 140


title: MR186

description: Library name: Sample 141


title: DAR Day 8 autologous PBMC culture replicate 2

description:
Library name: B2
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 8, replicate 2.


title: MR112

description: Library name: Sample 139


title: DAR Day 8 CLL B-cell monoculture replicate 1

description:
Library name: C2
DAR patient CLL sample, purified CLL B-cell monoculture, Day 8, replicate 1.


title: DAR Day 4 CLL B-cell monoculture replicate 2

description:
Library name: H1
DAR patient CLL sample, purified CLL B-cell monoculture, Day 4, replicate 2.


title: 623-MR185

description: Library name: Sample 137


title: MR_114

description: Library name: Sample 136

value: Secretory


title: DAR Day 8 autologous PBMC culture replicate 1

description:
Library name: A2
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 8, replicate 1.


title: DAR Day 4 autologous PBMC culture replicate 2

description:
Library name: F1
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 4, replicate 2.


title: MR245

description: Library name: Sample 135


title: MR116

description: Library name: Sample 134


title: DAR Day 4 autologous PBMC culture replicate 1

description:
Library name: E1
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 4, replicate 1.


title: DAR Day 1 CLL B-cell monoculture replicate 2

description:
Library name: D1
DAR patient CLL sample, purified CLL B-cell monoculture, Day 1, replicate 2.


title: 814-MR243

description: Library name: Sample 132


title: 379-MR115

description: Library name: Sample 133


title: DAR Day 1 CLL B-cell monoculture replicate 1

description:
Library name: C1
DAR patient CLL sample, purified CLL B-cell monoculture, Day 1, replicate 1.


title: DAR Day 1 autologous PBMC culture replicate 2

description:
Library name: B1
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 1, replicate 2.


title: 491-MR148

description: Library name: Sample 129

value: normal

value: normal/stable


title: MR226

description: Library name: Sample 130

value: hyperplasia


title: DAR Day 1 autologous PBMC culture replicate 1

description:
Library name: A1
DAR patient CLL sample in autologous PBMC culture (all peripheral blood mononuclear cells), Day 1, replicate 1.


title: 625-MR187

description: Library name: Sample 131


title: Patient_7_8_Day_1_3_7_MixC-CITESEQ

city: New Haven

first: Jonathan

middle: Howard

last: DeLong

state: CT

address: 300 George St Ste 353

department: Neurology

institute: Yale University

description:
Library name: Sample 22
10X Genomics
Patient_7_8_Day_1_3_7_MixC_barcodes.tsv.gz
Patient_7_8_Day_1_3_7_MixC_features.tsv.gz
Patient_7_8_Day_1_3_7_MixC_matrix.mtx.gz

library_source: other

data_processing:
Reads were aligned using CellRanger v7.1.0, using the human reference transcriptome GRCh38-2020-A.
Assembly: Human GRCh38-2020-A
Supplementary files format and content: Feature Barcode Market Exchange Matrices (MEX) produced by CellRanger v7.1.0
Library strategy: CITE-seq

molecule: protein

extract_protocol:
PBMC were isolated and cryopreserved. PBMC were thawed in batches, with all timepoints for a given patient thawed and analyzed at once. Five total batches: Patient 2, Patients 3 & 4, Patient 5, Patient 6, Patients 7 & 8. Cells were then stained with fluorescently-labeled antibodies specific for canonical cell lineage markers, fixable Live/Dead stain, and in some cases hashing antibodies. Live cells were isolated via FACS Aria before analysis by 10X.
Library construction was performed according to manufacturer's protocol using 10X genomics single cell 3' v3 chemistry.

treatment_protocol: Patients were treated with BAF312 or placebo control

value: PBMC

tag: library type

value: HTO

tag: hto

value: TotalSeq-B251 anti-Human Hashtag 1 (Patient 7 Day 1), TotalSeq-B252 anti-Human Hashtag 2 (Patient 7 Day 3), TotalSeq-B253 anti-Human Hashtag 3 (Patient 7 Day 7), TotalSeq-B254 anti-Human Hashtag 4 (Patient 8 Day 1), TotalSeq-B255 anti-Human Hashtag 5 (Patient 8 Day 3), TotalSeq-B256 anti-Human Hashtag 6 (Patient 8 Day 7)


title: Patient_7_8_Day_1_3_7_MixB-CITESEQ

description:
Library name: Sample 20
10X Genomics
Patient_7_8_Day_1_3_7_MixB_barcodes.tsv.gz
Patient_7_8_Day_1_3_7_MixB_features.tsv.gz
Patient_7_8_Day_1_3_7_MixB_matrix.mtx.gz

value: Blood

tag: treatment


title: MR225

description: Library name: Sample 128

value: Inflammatory


title: 337-MR105

description: Library name: Sample 126


title: Patient_7_8_Day_1_3_7_MixC

description:
Library name: Sample 21
10X Genomics
Patient_7_8_Day_1_3_7_MixC_feature_ref.csv

library_source: transcriptomic single cell

data_processing:
Reads were aligned using CellRanger v7.1.0, using the human reference transcriptome GRCh38-2020-A.
Assembly: Human GRCh38-2020-A
Supplementary files format and content: Feature Barcode Market Exchange Matrices (MEX) produced by CellRanger v7.1.0

value: mRNA


title: MR241

description: Library name: Sample 138

value: mild dysplasia


title: DAR Day 8 CLL B-cell monoculture replicate 2

description:
Library name: D2
DAR patient CLL sample, purified CLL B-cell monoculture, Day 8, replicate 2.

value: Primary cells

tag: batch


title: MR_269

description: Library name: Sample 127


title: Patient_7_8_Day_1_3_7_MixB

description:
Library name: Sample 19
10X Genomics
Patient_7_8_Day_1_3_7_MixB_feature_ref.csv


title: Patient_7_8_Day_1_3_7_MixA-CITESEQ

description:
Library name: Sample 18
10X Genomics
Patient_7_8_Day_1_3_7_MixA_barcodes.tsv.gz
Patient_7_8_Day_1_3_7_MixA_features.tsv.gz
Patient_7_8_Day_1_3_7_MixA_matrix.mtx.gz


title: MR237

description: Library name: Sample 124


title: MR2R-29

description: Library name: Sample 125


title: MR2R-27

description: Library name: Sample 123

value: metaplasia

value: Normal


title: Patient_7_8_Day_1_3_7_MixA

description:
Library name: Sample 17
10X Genomics
Patient_7_8_Day_1_3_7_MixA_feature_ref.csv


title: Patient_6_Day_1_3_7_MixB-CITESEQ

description:
Library name: Sample 16
10X Genomics
Patient_6_Day_1_3_7_MixB_barcodes.tsv.gz
Patient_6_Day_1_3_7_MixB_features.tsv.gz
Patient_6_Day_1_3_7_MixB_matrix.mtx.gz

value: Placebo

value: TotalSeq-B254 anti-Human Hashtag 4 (Patient 6 Day 1), TotalSeq-B255 anti-Human Hashtag 5 (Patient 6 Day 3), TotalSeq-B256 anti-Human Hashtag 6 (Patient 6 Day 7)


title: MR236

description: Library name: Sample 122

value: bronchial biopsy

value: progressive/persistent


title: Patient_6_Day_1_3_7_MixB

description:
Library name: Sample 15
10X Genomics
Patient_6_Day_1_3_7_MixB_feature_ref.csv


title: DAR Day 4 CLL B-cell monoculture replicate 1

description:
Library name: G1
DAR patient CLL sample, purified CLL B-cell monoculture, Day 4, replicate 1.

value: Chronic lymphocytic leukaemia B cells

value: CLL B-cell monoculture


title: Patient_6_Day_1_3_7_MixA-CITESEQ

description:
Library name: Sample 14
10X Genomics
Patient_6_Day_1_3_7_MixA_barcodes.tsv.gz
Patient_6_Day_1_3_7_MixA_features.tsv.gz
Patient_6_Day_1_3_7_MixA_matrix.mtx.gz


title: Patient_6_Day_1_3_7_MixA

description:
Library name: Sample 13
10X Genomics
Patient_6_Day_1_3_7_MixA_feature_ref.csv


title: MR_161

description: Library name: Sample 120

value: normal

value: Secretory


title: MR177

description: Library name: Sample 121

value: moderate dysplasia

value: regressive


title: Patient_5_Day_7

description:
Library name: Sample 12
10X Genomics

value: Blood

value: PBMC


title: 383-MR117

description: Library name: Sample 119

value: severe dysplasia

value: Proliferative


title: MR2R-30

description: Library name: Sample 118

value: Inflammatory

value: unknown


title: MR_179

description: Library name: Sample 116

value: metaplasia

value: Normal

value: normal/stable


title: MR_238

description: Library name: Sample 117

value: bronchial biopsy


title: Patient_5_Day_1

description:
Library name: Sample 10
10X Genomics

value: Placebo

value: mRNA


title: 541-MR162

description: Library name: Sample 115


title: Patient_5_Day_3

description:
Library name: Sample 11
10X Genomics


title: Patient_3_4_Day_1_3_7_MixC-CITESEQ

description:
Library name: Sample 9
10X Genomics
Patient_3_4_Day_1_3_7_MixC_barcodes.tsv.gz
Patient_3_4_Day_1_3_7_MixC_features.tsv.gz
Patient_3_4_Day_1_3_7_MixC_matrix.mtx.gz

value: HTO

value: TotalSeq-A251 anti-Human Hashtag 1 (Patient 3 Day 1), TotalSeq-A252 anti-Human Hashtag 2 (Patient 3 Day 3), TotalSeq-A253 anti-Human Hashtag 3 (Patient 3 Day 7), TotalSeq-A254 anti-Human Hashtag 4 (Patient 4 Day 1), TotalSeq-A255 anti-Human Hashtag 5 (Patient 4 Day 3), TotalSeq-A256 anti-Human Hashtag 6 (Patient 4 Day 7)


title: Patient_3_4_Day_1_3_7_MixB

description:
Library name: Sample 6
10X Genomics
Patient_3_4_Day_1_3_7_MixB_feature_ref.csv


title: 600-MR178

description: Library name: Sample 112

value: normal


title: MR2R-28

description: Library name: Sample 113


title: MR_233

description: Library name: Sample 111


title: 384-MR118

description: Library name: Sample 114

value: moderate dysplasia

value: progressive/persistent


title: Patient_3_4_Day_1_3_7_MixB-CITESEQ

description:
Library name: Sample 7
10X Genomics
Patient_3_4_Day_1_3_7_MixB_barcodes.tsv.gz
Patient_3_4_Day_1_3_7_MixB_features.tsv.gz
Patient_3_4_Day_1_3_7_MixB_matrix.mtx.gz

value: Blood


title: Patient_3_4_Day_1_3_7_MixC

description:
Library name: Sample 8
10X Genomics
Patient_3_4_Day_1_3_7_MixC_feature_ref.csv

value: PBMC


title: Patient_3_4_Day_1_3_7_MixA-CITESEQ

description:
Library name: Sample 5
10X Genomics
Patient_3_4_Day_1_3_7_MixA_barcodes.tsv.gz
Patient_3_4_Day_1_3_7_MixA_features.tsv.gz
Patient_3_4_Day_1_3_7_MixA_matrix.mtx.gz


title: Patient_3_4_Day_1_3_7_MixA

description:
Library name: Sample 4
10X Genomics
Patient_3_4_Day_1_3_7_MixA_feature_ref.csv


title: MR249

description: Library name: Sample 109

value: Secretory


title: MR248

description: Library name: Sample 108

value: hyperplasia