title: Batch2_SST_PTZ_Rep1

description:
NS68_M5
Max_NS68_raw.txt

value: PTZ


title: Batch2_SST_Saline_Rep4

status: Public on Jun 05 2024

type: SRA

city: La Jolla

first: Anton

last: Maximov

state: CA

address: 10550 North Torrey OPines Rd

department: Neuroscince

country: USA

institute: Scripps Research

description:
NS68_M4
Max_NS68_raw.txt

library_source: transcriptomic

data_processing:
The reads were trimmed from adapter sequences using cutadapt 1.18 with Python 3.6.3. The trimmed reads were mapped to the reference genome using the STAR aligner 2.5.2a and gene abundance was estimated with python 2.7.11, and HTSeq 0.11.0. Differential expression analysis was performed in the R package DESeq2. DESeq2 first adjusts read counts based on a normalization factor that accounts for sample size. This was followed by dispersion estimates based on a negative binomial model which accounts for genes with very few counts. Finally, the Wald test was performed to test for statistical significance. Genes with adjusted p-values (padj) of <0.05 were identified as differentially expressed. To remove genes with high fold changes due to low expression, a minimum normalized expression level (basemean) filter of 50 was added. The filtered data were used to generate volcano plots and heatmaps.
Assembly: mm10 for Batch1 and 2,  GRCm39 for Batch3, 4 and 5.
Supplementary files format and content: Tab-delimited TXT files includes raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Cortex and hippocampus

extract_protocol:
Isolation of mRNA with RiboTag:
Cortices of p60 PvalbCre/RiboTag and SstCre/RiboTag mice were dissected in ice-cold PBS and homogenized in the buffer containing 100 mM KCl, 50 mM Tris-HCl pH 7.4, 12 mM MgCl2, 100 g/ml cycloheximide (Sigma), 1 mg/ml heparin (Sigma), 1x complete mini, EDTA-free protease inhibitor cocktail (Roche), 200 units/ml RNasin© plus inhibitor (Promega) and 1 mM DTT (Sigma) (500 µl ~3% w/v). The lysate was centrifuged at 2,000g for 10 minutes at 4°C. Igepal-CA380 was then added to the supernatant at the final concentration of 1%. The lysate was briefly incubated on ice and then centrifuged at 12,000g for 10 minutes at 4°C. 25 µl of the supernatant was collected as input sample. 30 µl/ml of anti-HA coupled magnetic beads (Pierce) were then added to the remaining supernatant. Incubation was performed on a rotator for 3 hours at 4°C. The beads were washed four times in the high salt buffer containing 350 mM KCl, 1% Igepal-CA380, 50 mM Tris-HCl, pH7.4, 12 mM MgCl2, 100 µg/ml Cycloheximide (Sigma) and 1 mM DTT (Sigma). Ribosomes were eluted in 350 µl of RLT plus buffer (Qiagen). RNA purification was performed using RNeasy Plus Mini kit (Qiagen) following the manufacturers’ instructions. For qPCR, 20 ng of total RNA was reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems). qPCR quality controls were performed with the following primers:                                                                                Fos
Forward: 5′- GGGACAGCCTTTCCTACTACC-3′
Reverse: 5′- AGATCTGCGCAAAAGTCCTG-3′
Nr4a1
Forward: 5′- TTGAGTTCGGCAAGCCTACC-3′
Reverse: 5′- GTGTACCCGTCCATGAAGGTG-3′
Gapdh
Forward: 5′- TCAACGGGAAGCCCATCA-3′
Reverse: 5′- CTCGTGGTTCACACCCATCA-3′
Syt2
Forward: 5′- AGAACCTGGGCAAATTGCAGT-3′
Reverse: 5′- CCTAACTCCTGGTATGGCACC-3′
Pvalb
Forward: 5′- CATTGAGGAGGATGAGCTG-3′
Reverse: 5′- AGTGGAGAATTCTTCAACCC-3′
Lhx6
Forward: 5′- CTACTTCAGCCGATTTGGAACC-3′
Reverse: 5′- GCAAAGCACTTTCTCCTCAACG-3′
RNA-seq was performed at the TSRI Next Generation Sequencing Core on the Illumina HiSeq platform. The libraries were generated, barcoded, and sequenced according to the manufacturers’ recommendations.
Sequencing libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

tag: tissue

value: Cortex and hippocampus

tag: cell line

value: C57/BL6 mouse

tag: cell type

value: SST+ neuron

tag: genotype

tag: treatment

value: Saline


title: Batch2_SST_PTZ_Rep3

description:
NS68_M8
Max_NS68_raw.txt


title: Batch2_SST_Saline_Rep1

description:
NS68_M1
Max_NS68_raw.txt


title: Batch2_PVR_Saline_Rep2

description:
NS68_M10
Max_NS68_raw.txt

value: PV+ neuron


title: Batch1_PVR_PTZ_Rep3

description:
NS46_S7
NS046_raw-counts_gt40.txt


title: Batch1_PVR_PTZ_Rep4

description:
NS46_S8
NS046_raw-counts_gt40.txt


title: Batch2_SST_Saline_Rep3

description:
NS68_M3
Max_NS68_raw.txt


title: Batch1_PVR_PTZ_Rep2

description:
NS46_S4
NS046_raw-counts_gt40.txt


title: Batch1_PVR_PTZ_Rep1

description:
NS46_S2
NS046_raw-counts_gt40.txt


title: Batch1_PVR_Saline_Rep1

description:
NS46_S1
NS046_raw-counts_gt40.txt


title: Batch1_PVR_Saline_Rep3

description:
NS46_S5
NS046_raw-counts_gt40.txt


title: Mouse with wild-type AEG-1

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

description: FFPE tissue sequencing

data_processing:
Raw reads obtained from the 10x Visium library were processed using Space Ranger v2.0.1, which aligned the sequencing reads to the Gex-mm10-2020-A reference genome and probe set to generate gene-count matrices.
1. Filtered feature-barcode matrices and spatial coordinates were imported into R using the Seurat package (v4.3.0). 2. SCTransformation was applied to normalize gene expression data. 3. Samples were then merged into a single object for joint dimensional reduction and clustering. 4. Clustering.
Assembly: Gex-mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: 2318.tif: H&E image for sample WT_2318
Supplementary files format and content: 2319.2.tif: H&E image for sample C75S_2319
Library strategy: Spatial transcriptomics

molecule: total RNA

source_name: Liver

growth_protocol: Naïve mouse liver samples were used.

extract_protocol:
Livers were harvested after anesthesia
Spatial transcriptomics sequencing libraries were prepared using 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to the manufacturer's instruction

treatment_protocol: No treatment

value: Liver

value: WT


title: WT cells, 1hr LipidA, PHF10 ChIP

first: Jingwen

last: Liao

address: 10010 N Torrey Pines Rd

institute: Salk Institute

library_source: genomic

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ChIP-seq peaks were called using findPeaks within HOMER using -style factor and an -i input control. Differential ChIP peaks were called using getDiffExpression.pl with fold change ≥ 1.5 or ≤ 1.5
Metaplots were generated using annotatePeaks.pl with parameters -size 1000 and -hist 25. Heatmaps showing overlap of binding sites were generated using mergePeaks in HOMER with flag -matrix, which outputs hypergeometric P values of overlap and the observed/expected ratio of overlap. Peaks sets were annotated with HOMER, and visualizations were created using deepTools.
bigWig files were generated using makeUCSCfile program in HOMER using -style chipseq
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigWig (except for Input sample)

molecule: genomic DNA

source_name: BMDM

extract_protocol:
Cells were cross linked in 3 mM disuccinimidyl glutarate for 30 min then in 1% formaldehyde for 10 min at room temperature. After quenching with 125 mM glycine, the cells were washed in 1× PBS, pelleted, flash frozen in liquid nitrogen, and stored at 80 °C. Cell pellets were thawed on ice and incubated in lysis solution (50 mM Hepes KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min. The isolated nuclei were washed (10 mM TrisHCl pH 8, 1 mM EDTA, 0.5 mM EGTA, and 200 mM NaCl) and sheared in (0.1% SDS, 1 mM EDTA, and 10 mM TrisHCl pH 8) with the Covaris E229 sonicator for 10 min. After centrifugation, chromatin was immunoprecipitated overnight at 4 °C with respective antibody. The next day, the antibody-bound DNA was incubated with Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM Hepes KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS), washed, and treated with Proteinase K and RNase A and reverse cross linked.
Purified ChIP DNA was used for library generation (NEBNext Ultra II DNA Library Prep Kit for Illumina) according to manufacturer’s instructions

value: BMDM

tag: stimulation

value: 1hr LipidA

tag: antibody

value: Thermal Fisher #PA5-30678


title: WT cells, 4hr LipidA, PHF10 ChIP

value: 4hr LipidA


title: WT cells, 4hr LipidA, BRD9 ChIP


title: WT cells, 1hr LipidA, BRD9 ChIP


title: Batch1_PVR_Saline_Rep4

description:
NS46_S6
NS046_raw-counts_gt40.txt


title: Batch2_SST_PTZ_Rep2

description:
NS68_M6
Max_NS68_raw.txt


title: WT cells, 4hr LipidA, ARID1A ChIP

value: Cell Signaling #12354S


title: WT cells, 0hr LipidA, PHF10 ChIP

value: 0hr LipidA


title: WT cells, 0hr LipidA, BRD9 ChIP


title: WT cells, 1hr LipidA, ARID1A ChIP


title: WT cells, 0hr LipidA, ARID1A ChIP


title: WT cells, 0hr LipidA, input [Exp3_0hr_Ctrl_input]


title: Batch2_SST_Saline_Rep2

description:
NS68_M2
Max_NS68_raw.txt


title: WT cells, 4hr LipidA, input [Exp3_4hr_Ctrl_input]


title: WT cells, 1hr LipidA, input [Exp3_1hr_Ctrl_input]


title: WT cells, 4hr LipidA, BRD9 ChIP [Exp3_4hr_Ctrl_BRD9]


title: WT cells, 1hr LipidA, BRD9 ChIP [Exp3_1hr_Ctrl_BRD9]


title: Mouse with C75S mutant AEG-1

description: FFPE tissue sequencing


title: WT cells, 0hr LipidA, BRD9 ChIP [Exp3_0hr_Ctrl_BRD9]


title: Oocytes from atretic antral follicle_3

city: Hohhot

first: Song

last: Yukun

state: Inner Mongolia

address: Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction

country: China

institute: Inner Mongolia Agricultural University

data_processing:
Alignment with Reference Genome;Quantification of Gene Abundance;Differentially expressed genes (DEGs) Analysis
Assembly: Ovis_aries_rambouillet
Supplementary files format and content: FPKM

organism: Ovis aries

source_name: follicle

extract_protocol:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)

value: follicle

value: Oocyte

value: germ cells

tag: group

value: antral


title: Oocytes from atretic antral follicle_2


title: WT cells, 4hr LipidA, BRG1 ChIP [Exp3_4hr_Ctrl_BRG1]

value: Abcam #ab110641


title: Oocytes from atretic antral follicle_1


title: Oocytes from healthy antral follicle_2

value: healthy


title: Oocytes from healthy antral follicle_3


title: WT cells, 1hr LipidA, BRG1 ChIP [Exp3_1hr_Ctrl_BRG1]


title: Oocytes from healthy antral follicle_1


title: WT cells, 0hr LipidA, BRG1 ChIP [Exp3_0hr_Ctrl_BRG1]


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 2

city: Saint Louis

first: Farshid

last: Guilak

state: MO

address: 660 S Euclid Ave, Campus Box 8233

department: Dept of Orthopedics

institute: Washington University in St. Louis

data_processing:
Raw files were processed with Trim Galore! (Babraham Bioinformatics) to decrease noise and remove excess/low quality reads. Post-processing, these reads were aligned to the porcine reference genome (assembly: GCA_000003025.6 Sscrofa11.1.99) by STAR. Reads aligned with each annotated gene or transcript were counted using HTseq.
Assembly: GCA_000003025.6 Sscrofa11.1.99
Supplementary files format and content: .csv file contains raw gene counts for each sample

organism: Sus scrofa

source_name: femoral cartilage

growth_protocol: primary chondrocytes were cast in 2% agarose to form tissue engineered cartilage constructs. These constructs were cultured at 37°C and 5% CO2 in media consisting of DMEM-HG, 10% Fetal Bovine Serum (FBS), 7.5% HEPES Buffer, 5% MEM Non-Essential Amino Acids (MEM NEAA), and 5% Penicillin/Streptomycin (P/S)

extract_protocol:
RNA was isolated (~0.5ug from TRPV4 and IL-1 groups, ~100ng from PIEZO1 groups) from all tissues using a bead shaker and the Norgen Biotek RNA/protein purification plus kit (Norgen Total RNA kits).
For all TRPV4 and IL-1 groups: Library preparation was performed with 1 to 3ug of total RNA. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina-EpiCentre). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.
For all PIEZO1 groups: Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol:
To study TRPV4 activation and IL-1 inflammatory signalling, constructs were stimulated for 3 hours with cyclic, unconfined compressive loading (10% peak-to-peak deformation, 1 Hz) with or without TRPV4 antagonist GSK205 (10 mM) or treated with TRPV4 agonist GSK101 (1 nM) or 1 ng/mL of IL-1a. Vehicle controls were exposed to DMSO (1:1000 in media) but left free swelling. For both TRPV4 and IL-1 stimulation groups, tissue constructs were taken down at 3 hours and 9 hours post stimulation onset, flash frozen, and stored at -80C (n=4 per group).
To study PIEZO1 activation, PIEZO1 needed to be inhibited by siRNA transfection ,as no small molecule inhibitors of PIEZO1 are currently known. Cells were transfected (DharmaFECT Transfection Reagent, Dharmacon) with siRNA targeting PIEZO1 (siPIEZO1) [1], a non-targeting control siRNA (siNTC), or left non-transfected (NT). PIEZO1-targeting siRNA sequences included CAGCGAGAUCUCGCACUCCAUC (siPIEZO1a), UACGACCUGCUGCAGCUCCUG (siPIEZO1b), and  ACCCGCUGGCCAUGCAGUUCUU (siPIEZO1c) to target different transcript variants of PIEZO1 (custom siRNA, Dharmacon). These siRNAs were added to DMEM-HG for a final concentration of ~222 nM siPIEZO1a, ~278 nM siPEIZO1b, and ~278nM siPIEZO1c. Separately, DharmaFECT reagent was diluted 3:50 in DMEM-HG. Each solution was incubated at room temperature for 5 min. The two solutions were then mixed 1:1, and incubated at room temperature for 20 min. Lastly, 500mL of the siRNA/DharmaFECT solution was added to each well.
After siRNA transfection, constructs were subjected to a single round of quasi-static unconfined compression to 80% deformation (supraphysiologic range) at 1.9% deformation/min (~0.73 mm/sec), treated with PIEZO1 agonist Yoda1 (5 mM), or standard media with a DMSO vehicle control (1:1000) but left free swelling. This timepoint was chosen as it displayed the peak PIEZO1 knockdown in the siPIEZO1 group, similar to previous studies [1]. In response to stimulation, tissue constructs were taken down at 3 hours and 9 hours post stimulation onset, flash frozen, and stored at -80C (n=4 per group).

value: femoral cartilage

value: primary chondrocyte

tag: time point

value: 9 hours


title: WT cells, 4hr LipidA, PHF10 ChIP [Exp2_4hr_Ctrl_PHF10]


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 3


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 4

value: Supraphysiologic Load


title: WT cells, 0hr LipidA, input [Exp2_0hr_Ctrl_input]

value: WT


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 1


title: WT cells, 0hr LipidA, PHF10 ChIP [Exp2_0hr_Ctrl_PHF10]

value: BMDM


title: WT cells, 4hr LipidA, input [Exp1_4hr_Ctrl input]


title: BRDK98 treated cells, 0hr LipidA, input [Exp1_0hr_BRDK98 input]

value: BRDK98 treated


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 2


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 1


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 3


title: WT cells, 0hr LipidA, input [Exp1_0hr_Ctrl input]


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 4

value: Vehicle Control


title: WT cells, 1hr LipidA, input [Exp1_1hr_Ctrl input]

value: 1hr LipidA


title: BRDK98 treated cells, 4hr LipidA, ARID1A ChIP [Exp1_4hr_BRDK98_ARID1A]

value: 4hr LipidA

value: Cell Signaling #12354S


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 3


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 4


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 2


title: BRDK98 treated cells, 0hr LipidA, ARID1A ChIP [Exp1_0hr_BRDK98_ARID1A]

value: 0hr LipidA


title: transduced with non-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 4

value: siNTC


title: transduced with non-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 2


title: WT cells, 0hr LipidA, ARID1A ChIP [Exp1_0hr_Ctrl_ARID1A]


title: WT cells, 0hr LipidA, input [Exp2_input]

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ChIP-seq peaks were called using findPeaks within HOMER using -style factor and an -i input control. Differential ChIP peaks were called using getDiffExpression.pl with fold change ≥ 1.5 or ≤ 1.5
Metaplots were generated using annotatePeaks.pl with parameters -size 1000 and -hist 25. Heatmaps showing overlap of binding sites were generated using mergePeaks in HOMER with flag -matrix, which outputs hypergeometric P values of overlap and the observed/expected ratio of overlap. Peaks sets were annotated with HOMER, and visualizations were created using deepTools.
bigWig files were generated using makeUCSCfile program in HOMER using -style chipseq
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig (except for input sample)

extract_protocol: Purified ChIP DNA was used for library generation (NEBNext Ultra II DNA Library Prep Kit for Illumina) according to manufacturer’s instructions

treatment_protocol: Cells were cross linked in 3 mM disuccinimidyl glutarate for 30 min then in 1% formaldehyde for 10 min at room temperature. After quenching with 125 mM glycine, the cells were washed in 1× PBS, pelleted, flash frozen in liquid nitrogen, and stored at 80 °C. Cell pellets were thawed on ice and incubated in lysis solution (50 mM Hepes KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min. The isolated nuclei were washed (10 mM TrisHCl pH 8, 1 mM EDTA, 0.5 mM EGTA, and 200 mM NaCl) and sheared in (0.1% SDS, 1 mM EDTA, and 10 mM TrisHCl pH 8) with the Covaris E229 sonicator for 10 min. After centrifugation, chromatin was immunoprecipitated overnight at 4 °C with respective antibody. The next day, the antibody-bound DNA was incubated with Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM Hepes KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS), washed, and treated with Proteinase K and RNase A and reverse cross linked.


title: WT cells, 1hr LipidA, ARID1A ChIP [Exp1_1hr_Ctrl_ARID1A]


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 1


title: BRDK98 treated cells, 4hr LipidA, input [Exp1_4hr_BRDK98 input]


title: Pbrm1-/- cells, 4hr LipidA, H3K27ac ChIP [Exp2_4hr_PBRM1KO]

value: Abcam #ab4729


title: dBrd9 treated cells, 4hr LipidA, H3K27ac ChIP [Exp2_4hr_dBrd9]


title: transduced with non-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 1


title: transduced with non-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 3


title: WT cells, 0hr LipidA, H3K27ac ChIP [Exp2_0hr_Ctrl]


title: WT cells, 4hr LipidA, H3K27ac ChIP [Exp2_4hr_Ctrl]


title: transduced with non-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 4


title: Arid1A-/- cells, 4hr LipidA, input [Exp1_4hr_ARID1AKO_input]


title: transduced with non-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 1


title: transduced with non-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 3


title: BRDK98 treated cells, 4hr LipidA, input [Exp1_4hr_BRDK98_input]


title: ACBI1 treated cells, 4hr LipidA, input [Exp1_4hr_ACBI1_input]

value: ACBI1 treated


title: transduced with non-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 4


title: BRM014 treated cells, 4hr LipidA, input [Exp1_4hr_BRM014_input]

value: BRM014 treated


title: WT cells, 4hr LipidA, ARID1A ChIP [Exp1_4hr_Ctrl_ARID1A]


title: WT cells, 4hr LipidA, input [Exp1_4hr_Ctrl_input]


title: transduced with non-targeting siRNA, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 3


title: transduced with non-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 2


title: WT cells, 0hr LipidA, input [Exp1_0hr_Ctrl_input]


title: non-transduced, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 4

value: WT/NT


title: BRDK98 treated cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_BRDK98_H3K27ac]


title: Arid1A-/- cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_ARID1AKO_H3K27ac]


title: non-transduced, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 3

value: femoral cartilage


title: non-transduced, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 2

value: primary chondrocyte


title: non-transduced, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 4

value: 9 hours


title: ACBI1 treated cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_ACBI1_H3K27ac]


title: BRM014 treated cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_BRM014_H3K27ac]


title: non-transduced, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 2

value: Supraphysiologic Load


title: transduced with non-targeting siRNA, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 2


title: WT cells, 0hr LipidA, H3K27ac ChIP [Exp1_0hr_Ctrl_H3K27ac]

value: WT


title: non-transduced, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 3


title: WT cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_Ctrl_H3K27ac]

value: BMDM


title: non-transduced, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 4


title: 34.5,tumor [DSP-1001660005323-A-E12]

type: RNA

city: New Orleans

first: Ruoxin

last: Lan

state: LA

address: 204 S Saratoga St, Apt 316

institute: Tulane University

description: A total of 116 regions of interest (ROIs) with the most representative tumor morphology for each case were selected from the 36 patients in our cohort.

hyb_protocol: RNA samples wer hybrizied with Nanostring GeoMx CTA probes according to the manufacturer's instruction.

scan_protocol: NGS readout was used. No scanning needed.

data_processing:
We used GeomxTools (version 3.1.1) package, NanoStringNCTools (version 1.7.1) package, and GeoMxWorkflows (version 1.3.1) in R software (version 4.1.2) to analyze GeoMx-NGS RNA Expression Data.
Quantile normalized gene expression matrix table (for 223 samples that passed the quality control)

organism: Homo sapiens

source_name: Pancreatic Ductal Adenocarcinoma

extract_protocol: For each case, one 5 um-thick FFPE section was prepared for the extraction of total RNA from the tumor area and the stroma area.

value: Pancreatic Ductal Adenocarcinoma

value: Treated

tag: tissue type

value: tumor


title: 34.4,stroma [DSP-1001660005323-A-E11]

value: stroma


title: non-transduced, supraphysiologic loading, t=9 hours post-onset of stimulation, sample 1


title: 34.5,stroma [DSP-1001660005323-A-F01]


title: transduced with non-targeting siRNA, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 1

value: Vehicle Control


title: non-transduced, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 1


title: non-transduced, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 2


title: Physiologic loading, t=9 hours post-onset of stimulation, sample 4

value: Phys. Load


title: Physiologic loading, t=9 hours post-onset of stimulation, sample 3


title: 34.3,tumor [DSP-1001660005323-A-E08]


title: 34.4,tumor [DSP-1001660005323-A-E10]


title: 34.3,stroma [DSP-1001660005323-A-E09]


title: 34.2,stroma [DSP-1001660005323-A-E07]


title: Physiologic loading, t=9 hours post-onset of stimulation, sample 2


title: Physiologic loading, t=9 hours post-onset of stimulation, sample 1


title: 34.1,tumor [DSP-1001660005323-A-E04]


title: 34.1,stroma [DSP-1001660005323-A-E05]


title: non-transduced, Yoda1 treatment, t=9 hours post-onset of stimulation, sample 1


title: 32.5,stroma [DSP-1001660005323-A-E03]

value: Naïve


title: 34.2,tumor [DSP-1001660005323-A-E06]


title: Physiologic loading plus GSK205 treatment, t=9 hours post-onset of stimulation, sample 2

value: Phys. Load + GSK205


title: Physiologic loading plus GSK205 treatment, t=9 hours post-onset of stimulation, sample 3


title: Physiologic loading plus GSK205 treatment, t=9 hours post-onset of stimulation, sample 4


title: Physiologic loading plus GSK205 treatment, t=9 hours post-onset of stimulation, sample 1


title: 32.4,stroma [DSP-1001660005323-A-E01]


title: non-transduced, DMSO vehicle control, t=9 hours post-onset of stimulation, sample 3


title: IL-1 treatment, t=9hours post-onset of stimulation, sample 3


title: 32.4,tumor [DSP-1001660005323-A-D12]


title: 32.3,stroma [DSP-1001660005323-A-D11]


title: IL-1 treatment, t=9hours post-onset of stimulation, sample 2


title: IL-1 treatment, t=9hours post-onset of stimulation, sample 1


title: 32.2,stroma [DSP-1001660005323-A-D09]


title: 32.2,tumor [DSP-1001660005323-A-D08]


title: DMSO vehicle control, t=9 hours post-onset of stimulation, sample 4


title: DMSO vehicle control, t=9 hours post-onset of stimulation, sample 3


title: 32.1,stroma [DSP-1001660005323-A-D07]


title: DMSO vehicle control, t=9 hours post-onset of stimulation, sample 2


title: 27.5,stroma [DSP-1001660005323-A-D05]


title: 32.3,tumor [DSP-1001660005323-A-D10]


title: DMSO vehicle control, t=9 hours post-onset of stimulation, sample 1


title: 32.1,tumor [DSP-1001660005323-A-D06]


title: 27.5,tumor [DSP-1001660005323-A-D04]


title: 32.5,tumor [DSP-1001660005323-A-E02]


title: GSK205 treatment, t=9 hours post-onset of stimulation, sample 4


title: GSK205 treatment, t=9 hours post-onset of stimulation, sample 2


title: 27.4,stroma [DSP-1001660005323-A-D03]


title: 27.4,tumor [DSP-1001660005323-A-D02]


title: 27.3,tumor [DSP-1001660005323-A-C12]


title: GSK205 treatment, t=9 hours post-onset of stimulation, sample 1


title: IL-1 treatment, t=9hours post-onset of stimulation, sample 4


title: 27.3,stroma [DSP-1001660005323-A-D01]


title: GSK101 treatment, t=9 hours post-onset of stimulation, sample 2


title: GSK101 treatment, t=9 hours post-onset of stimulation, sample 3


title: GSK101 treatment, t=9 hours post-onset of stimulation, sample 1


title: 27.1,stroma [DSP-1001660005323-A-C09]


title: 27.2,stroma [DSP-1001660005323-A-C11]


title: 27.1,tumor [DSP-1001660005323-A-C08]


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 4

value: 3 hours


title: 23.5,stroma [DSP-1001660005323-A-C07]


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 2


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 3


title: 23.5,tumor [DSP-1001660005323-A-C06]


title: GSK205 treatment, t=9 hours post-onset of stimulation, sample 3


title: 23.4,tumor [DSP-1001660005323-A-C04]


title: 23.3,tumor [DSP-1001660005323-A-C02]


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 4


title: GSK101 treatment, t=9 hours post-onset of stimulation, sample 4


title: 23.3,stroma [DSP-1001660005323-A-C03]


title: transduced with PIEZO1-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 1


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 2


title: 23.4,stroma [DSP-1001660005323-A-C05]


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 4


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 3


title: 23.2,tumor [DSP-1001660005323-A-B12]


title: transduced with PIEZO1-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 1


title: 23.2,stroma [DSP-1001660005323-A-C01]


title: 27.2,tumor [DSP-1001660005323-A-C10]


title: 23.1,stroma [DSP-1001660005323-A-B11]


title: 23.1,tumor [DSP-1001660005323-A-B10]


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 2


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 3


title: transduced with PIEZO1-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 1


title: 9.5,stroma [DSP-1001660005323-A-B09]


title: 9.5,tumor [DSP-1001660005323-A-B08]


title: transduced with non-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 4

value: siNTC


title: 9.4,tumor [DSP-1001660005323-A-B06]


title: transduced with non-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 3


title: transduced with non-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 2


title: transduced with non-targeting siRNA, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 1


title: 9.3,stroma [DSP-1001660005323-A-B05]


title: 9.3,tumor [DSP-1001660005323-A-B04]


title: transduced with non-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 4


title: 9.2,stroma [DSP-1001660005323-A-B03]


title: transduced with non-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 2


title: 9.2,tumor [DSP-1001660005323-A-B02]


title: transduced with non-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 4


title: 9.1,stroma [DSP-1001660005323-A-B01]


title: transduced with non-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 1


title: transduced with non-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 3


title: 5.5,stroma [DSP-1001660005323-A-A11]


title: transduced with non-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 2


title: 5.4,tumor [DSP-1001660005323-A-A08]


title: 5.5,tumor [DSP-1001660005323-A-A10]


title: transduced with non-targeting siRNA, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 1


title: non-transduced, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 4

value: WT/NT


title: non-transduced, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 2

value: femoral cartilage


title: 5.3,tumor [DSP-1001660005323-A-A06]


title: 5.4,stroma [DSP-1001660005323-A-A09]


title: 5.2,stroma [DSP-1001660005323-A-A05]


title: non-transduced, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 4

value: primary chondrocyte


title: 9.4,stroma [DSP-1001660005323-A-B07]


title: 5.2,tumor [DSP-1001660005323-A-A04]


title: 5.1,stroma [DSP-1001660005323-A-A03]


title: 5.1,tumor [DSP-1001660005323-A-A02]


title: transduced with non-targeting siRNA, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 3


title: non-transduced, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 1


title: 9.1,tumor [DSP-1001660005323-A-A12]


title: No Template Control,A [DSP-1001660005323-A-A01]

value: No Template Control


title: non-transduced, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 3


title: 59.3,tumor [DSP-1001660005322-B-H06]


title: 59.2,stroma [DSP-1001660005322-B-H05]


title: 59.3,stroma [DSP-1001660005322-B-H07]


title: non-transduced, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 2

value: Supraphysiologic Load


title: 5.3,stroma [DSP-1001660005323-A-A07]


title: non-transduced, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 1


title: non-transduced, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 2


title: non-transduced, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 3


title: 59.1,stroma [DSP-1001660005322-B-H03]


title: 59.2,tumor [DSP-1001660005322-B-H04]


title: 59.1,tumor [DSP-1001660005322-B-H02]


title: 58.3,stroma [DSP-1001660005322-B-H01]


title: Physiologic loading, t=3 hours post-onset of stimulation, sample 3


title: Physiologic loading, t=3 hours post-onset of stimulation, sample 2


title: Physiologic loading, t=3 hours post-onset of stimulation, sample 1


title: non-transduced, Yoda1 treatment, t=3 hours post-onset of stimulation, sample 1


title: 58.3,tumor [DSP-1001660005322-B-G12]


title: non-transduced, supraphysiologic loading, t=3 hours post-onset of stimulation, sample 3


title: 58.2,stroma [DSP-1001660005322-B-G11]


title: Physiologic loading plus GSK205 treatment, t=3 hours post-onset of stimulation, sample 3


title: 58.1,stroma [DSP-1001660005322-B-G09]


title: Physiologic loading plus GSK205 treatment, t=3 hours post-onset of stimulation, sample 2


title: Physiologic loading plus GSK205 treatment, t=3 hours post-onset of stimulation, sample 1


title: 58.1,tumor [DSP-1001660005322-B-G08]


title: 64.4,stroma [DSP-1001660005322-B-G07]


title: 64.3,stroma [DSP-1001660005322-B-G05]


title: non-transduced, DMSO vehicle control, t=3 hours post-onset of stimulation, sample 4


title: IL-1 treatment, t=3 hours post-onset of stimulation, sample 4


title: 64.2,tumor [DSP-1001660005322-B-G02]


title: DMSO vehicle control, t=3 hours post-onset of stimulation, sample 3


title: DMSO vehicle control, t=3 hours post-onset of stimulation, sample 2


title: IL-1 treatment, t=3 hours post-onset of stimulation, sample 3


title: DMSO vehicle control, t=3 hours post-onset of stimulation, sample 1


title: Physiologic loading plus GSK205 treatment, t=3 hours post-onset of stimulation, sample 4


title: 63.3,stroma [DSP-1001660005322-B-F11]


title: IL-1 treatment, t=3 hours post-onset of stimulation, sample 2


title: GSK205 treatment, t=3 hours post-onset of stimulation, sample 4


title: IL-1 treatment, t=3 hours post-onset of stimulation, sample 1


title: Physiologic loading, t=3 hours post-onset of stimulation, sample 4


title: DMSO vehicle control, t=3 hours post-onset of stimulation, sample 4


title: 64.1,stroma [DSP-1001660005322-B-G01]


title: GSK205 treatment, t=3 hours post-onset of stimulation, sample 2


title: 64.1,tumor [DSP-1001660005322-B-F12]


title: 63.2,stroma [DSP-1001660005322-B-F09]


title: 63.2,tumor [DSP-1001660005322-B-F08]


title: 64.4,tumor [DSP-1001660005322-B-G06]


title: 64.3,tumor [DSP-1001660005322-B-G04]


title: 63.3,tumor [DSP-1001660005322-B-F10]


title: 58.2,tumor [DSP-1001660005322-B-G10]


title: GSK101 treatment, t=3 hours post-onset of stimulation, sample 4


title: 63.1,stroma [DSP-1001660005322-B-F07]


title: GSK205 treatment, t=3 hours post-onset of stimulation, sample 1


title: GSK101 treatment, t=3 hours post-onset of stimulation, sample 2


title: 64.2,stroma [DSP-1001660005322-B-G03]


title: GSK101 treatment, t=3 hours post-onset of stimulation, sample 3


title: 63.1,tumor [DSP-1001660005322-B-F06]


title: 57.3,stroma [DSP-1001660005322-B-F05]


title: 57.3,tumor [DSP-1001660005322-B-F04]


title: qNSCs, P7 (S143)

city: Philadelphia

first: Dennisse

last: Jimenez-Cyrus

state: PA

address: 415 Curie Blvd

department: Neuroscience

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
RSEM (Cole Dewey et al. 2011) to map and calculate the TPM
Assembly: mm10
Supplementary files format and content: text file with TPM.

source_name: brain

extract_protocol: Single cells were captured using FACS and cDNA processed using SMART-Seq2 protocol. Libraries constructed Tn5 enzyme-buffer system.

tag: strain

tag: reporter

value: Hopx-GFP

tag: age

value: brain

tag: tissue compartment

value: Dentate Gyrus

value: qNSCs


title: 57.2,tumor [DSP-1001660005322-B-F02]

value: Pancreatic Ductal Adenocarcinoma

value: tumor


title: GSK101 treatment, t=3 hours post-onset of stimulation, sample 1


title: qNSCs, P7 (S140)


title: qNSCs, P7 (S142)


title: 57.2,stroma [DSP-1001660005322-B-F03]

value: stroma


title: 56.3,stroma [DSP-1001660005322-B-E11]

value: Treated


title: 57.1,tumor [DSP-1001660005322-B-E12]

value: Naïve


title: GSK205 treatment, t=3 hours post-onset of stimulation, sample 3


title: 57.1,stroma [DSP-1001660005322-B-F01]


title: qNSCs, P7 (S139)


title: qNSCs, P7 (S141)


title: qNSCs, P7 (S135)


title: 56.1,stroma [DSP-1001660005322-B-E07]


title: 56.2,stroma [DSP-1001660005322-B-E09]


title: 56.2,tumor [DSP-1001660005322-B-E08]


title: qNSCs, P7 (S132)


title: qNSCs, P7 (S137)


title: 56.3,tumor [DSP-1001660005322-B-E10]


title: 55.2,stroma [DSP-1001660005322-B-E03]


title: qNSCs, P7 (S134)


title: 56.1,tumor [DSP-1001660005322-B-E06]


title: qNSCs, P7 (S133)


title: qNSCs, P7 (S129)


title: 55.3,stroma [DSP-1001660005322-B-E05]


title: qNSCs, P7 (S130)


title: qNSCs, P7 (S131)


title: 55.3,tumor [DSP-1001660005322-B-E04]


title: qNSCs, P7 (S128)


title: 54.3,tumor [DSP-1001660005322-B-D10]


title: 55.1,tumor [DSP-1001660005322-B-D12]


title: qNSCs, P7 (S126)


title: qNSCs, P7 (S125)


title: qNSCs, P7 (S123)


title: 54.3,stroma [DSP-1001660005322-B-D11]


title: qNSCs, P7 (S122)


title: 54.1,stroma [DSP-1001660005322-B-D07]


title: 55.2,tumor [DSP-1001660005322-B-E02]


title: 54.1,tumor [DSP-1001660005322-B-D06]


title: 55.1,stroma [DSP-1001660005322-B-E01]


title: qNSCs, P7 (S124)


title: 49.3,stroma [DSP-1001660005322-B-D05]


title: 54.2,tumor [DSP-1001660005322-B-D08]


title: qNSCs, P7 (S121)


title: qNSCs, P7 (S120)


title: 49.3,tumor [DSP-1001660005322-B-D04]


title: qNSCs, P7 (S116)


title: 49.2,tumor [DSP-1001660005322-B-D02]


title: qNSCs, P7 (S114)


title: 54.2,stroma [DSP-1001660005322-B-D09]


title: qNSCs, P7 (S113)


title: 49.2,stroma [DSP-1001660005322-B-D03]


title: 49.1,stroma [DSP-1001660005322-B-D01]


title: qNSCs, P7 (S112)


title: qNSCs, P7 (S111)


title: 48.2,tumor [DSP-1001660005322-B-C08]


title: qNSCs, P7 (S110)


title: qNSCs, P7 (S105)


title: qNSCs, P7 (S108)


title: 48.3,stroma [DSP-1001660005322-B-C11]


title: 48.3,tumor [DSP-1001660005322-B-C10]


title: qNSCs, P7 (S117)


title: qNSCs, P7 (S104)


title: qNSCs, P7 (S106)


title: qNSCs, P7 (S103)


title: 41.3,stroma [DSP-1001660005322-B-C05]


title: 48.1,tumor [DSP-1001660005322-B-C06]


title: qNSCs, P7 (S101)


title: qNSCs, P7 (S102)


title: 41.3,tumor [DSP-1001660005322-B-C04]


title: 41.2,stroma [DSP-1001660005322-B-C03]


title: qNSCs, P7 (S99)


title: qNSCs, P7 (S97)


title: 41.2,tumor [DSP-1001660005322-B-C02]


title: qNSCs, P7 (S96)


title: qNSCs, P7 (S93)


title: 41.1,tumor [DSP-1001660005322-B-B12]


title: qNSCs, P7 (S95)


title: 41.1,stroma [DSP-1001660005322-B-C01]


title: 49.1,tumor [DSP-1001660005322-B-C12]


title: qNSCs, P7 (S94)


title: 40.3,stroma [DSP-1001660005322-B-B11]


title: 48.2,stroma [DSP-1001660005322-B-C09]


title: 48.1,stroma [DSP-1001660005322-B-C07]


title: 40.3,tumor [DSP-1001660005322-B-B10]


title: qNSCs, P7 (S90)


title: qNSCs, P7 (S89)


title: qNSCs, P7 (S88)


title: 40.1,stroma [DSP-1001660005322-B-B07]


title: 40.2,tumor [DSP-1001660005322-B-B08]


title: qNSCs, P7 (S81)


title: qNSCs, P7 (S85)


title: 40.1,tumor [DSP-1001660005322-B-B06]


title: qNSCs, P7 (S86)


title: qNSCs, P7 (S79)


title: 39.3,stroma [DSP-1001660005322-B-B05]


title: 39.2,tumor [DSP-1001660005322-B-B02]


title: 39.3,tumor [DSP-1001660005322-B-B04]


title: 39.2,stroma [DSP-1001660005322-B-B03]


title: qNSCs, P7 (S78)


title: qNSCs, P7 (S77)


title: 39.1,stroma [DSP-1001660005322-B-B01]


title: 39.1,tumor [DSP-1001660005322-B-A12]


title: qNSCs, P7 (S76)


title: 40.2,stroma [DSP-1001660005322-B-B09]


title: 35.2,stroma [DSP-1001660005322-B-A11]


title: 35.2,tumor [DSP-1001660005322-B-A10]


title: qNSCs, P3 (S224)


title: 35.1,tumor [DSP-1001660005322-B-A08]


title: qNSCs, P7 (S74)


title: qNSCs, P3 (S72)


title: No Template Control,B [DSP-1001660005322-B-A01]


title: qNSCs, P7 (S87)


title: qNSCs, P3 (S71)


title: 35.1,stroma [DSP-1001660005322-B-A09]


title: 83.3,tumor [DSP-1001660005320-D-H12]


title: qNSCs, P3 (S70)


title: 83.2,stroma [DSP-1001660005320-D-H11]


title: qNSCs, P3 (S69)


title: 83.2,tumor [DSP-1001660005320-D-H10]


title: qNSCs, P3 (S67)


title: qNSCs, P3 (S66)


title: 67.3,stroma [DSP-1001660005320-D-H07]


title: qNSCs, P3 (S65)


title: qNSCs, P3 (S64)


title: qNSCs, P7 (S75)


title: 67.2,stroma [DSP-1001660005320-D-H05]


title: 67.2,tumor [DSP-1001660005320-D-H04]


title: qNSCs, P3 (S63)


title: 67.1,stroma [DSP-1001660005320-D-H03]


title: qNSCs, P3 (S58)


title: qNSCs, P3 (S60)


title: qNSCs, P3 (S61)


title: 92.3,stroma [DSP-1001660005320-D-H01]


title: 67.1,tumor [DSP-1001660005320-D-H02]


title: qNSCs, P3 (S57)


title: qNSCs, P3 (S55)


title: qNSCs, P3 (S54)


title: 92.2,stroma [DSP-1001660005320-D-G11]


title: qNSCs, P3 (S56)


title: 92.3,tumor [DSP-1001660005320-D-G12]


title: qNSCs, P3 (S53)


title: 83.1,stroma [DSP-1001660005320-D-H09]


title: 92.2,tumor [DSP-1001660005320-D-G10]


title: 83.1,tumor [DSP-1001660005320-D-H08]


title: qNSCs, P3 (S52)


title: qNSCs, P3 (S223)


title: 92.1,stroma [DSP-1001660005320-D-G09]


title: 92.1,tumor [DSP-1001660005320-D-G08]


title: 67.3,tumor [DSP-1001660005320-D-H06]


title: 76.3,stroma [DSP-1001660005320-D-G07]


title: qNSCs, P3 (S51)


title: 76.3,tumor [DSP-1001660005320-D-G06]


title: 76.2,tumor [DSP-1001660005320-D-G04]


title: qNSCs, P3 (S48)


title: 76.1,stroma [DSP-1001660005320-D-G03]


title: 76.2,stroma [DSP-1001660005320-D-G05]


title: qNSCs, P3 (S49)


title: qNSCs, P3 (S46)


title: 76.1,tumor [DSP-1001660005320-D-G02]


title: qNSCs, P3 (S45)


title: 89.2,tumor [DSP-1001660005320-D-F12]


title: 89.2,stroma [DSP-1001660005320-D-G01]


title: qNSCs, P3 (S221)


title: 89.1,tumor [DSP-1001660005320-D-F10]


title: 89.1,stroma [DSP-1001660005320-D-F11]


title: qNSCs, P3 (S44)


title: 87.2,stroma [DSP-1001660005320-D-F09]


title: qNSCs, P3 (S42)


title: qNSCs, P3 (S41)


title: qNSCs, P3 (S43)


title: 87.1,stroma [DSP-1001660005320-D-F07]


title: qNSCs, P3 (S40)


title: qNSCs, P3 (S38)


title: 87.1,tumor [DSP-1001660005320-D-F06]


title: qNSCs, P3 (S50)


title: qNSCs, P3 (S37)


title: 16.2,tumor [DSP-1001660005320-D-F04]


title: qNSCs, P3 (S47)


title: 16.2,stroma [DSP-1001660005320-D-F05]


title: qNSCs, P3 (S220)


title: qNSCs, P3 (S36)


title: 95.2,stroma [DSP-1001660005320-D-F01]


title: 16.1,tumor [DSP-1001660005320-D-F02]


title: 16.1,stroma [DSP-1001660005320-D-F03]


title: qNSCs, P3 (S34)


title: 95.2,tumor [DSP-1001660005320-D-E12]


title: 95.1,stroma [DSP-1001660005320-D-E11]


title: 95.1,tumor [DSP-1001660005320-D-E10]


title: qNSCs, P3 (S30)


title: qNSCs, P3 (S33)


title: 68.3,stroma [DSP-1001660005320-D-E09]


title: qNSCs, P3 (S29)


title: qNSCs, P3 (S31)


title: 68.3,tumor [DSP-1001660005320-D-E08]


title: 68.2,stroma [DSP-1001660005320-D-E07]


title: qNSCs, P3 (S27)


title: 87.2,tumor [DSP-1001660005320-D-F08]


title: 68.2,tumor [DSP-1001660005320-D-E06]


title: qNSCs, P3 (S28)


title: qNSCs, P3 (S26)


title: qNSCs, P3 (S25)


title: qNSCs, P3 (S24)


title: qNSCs, P3 (S23)


title: qNSCs, P3 (S35)


title: 68.1,tumor [DSP-1001660005320-D-E04]


title: 97.2,tumor [DSP-1001660005320-D-E02]


title: 68.1,stroma [DSP-1001660005320-D-E05]


title: 97.2,stroma [DSP-1001660005320-D-E03]


title: qNSCs, P3 (S21)


title: 79.2,stroma [DSP-1001660005320-D-D11]


title: qNSCs, P3 (S20)


title: 97.1,stroma [DSP-1001660005320-D-E01]


title: qNSCs, P3 (S19)


title: qNSCs, P3 (S32)


title: 97.1,tumor [DSP-1001660005320-D-D12]


title: qNSCs, P3 (S218)


title: 79.2,tumor [DSP-1001660005320-D-D10]


title: qNSCs, P3 (S18)


title: qNSCs, P3 (S17)


title: qNSCs, P3 (S15)


title: 79.1,tumor [DSP-1001660005320-D-D08]


title: 79.1,stroma [DSP-1001660005320-D-D09]


title: qNSCs, P3 (S14)


title: 53.3,tumor [DSP-1001660005320-D-D06]


title: 53.2,stroma [DSP-1001660005320-D-D05]


title: qNSCs, P3 (S13)


title: 53.1,stroma [DSP-1001660005320-D-D03]


title: qNSCs, P3 (S22)


title: qNSCs, P3 (S10)


title: 53.2,tumor [DSP-1001660005320-D-D04]


title: qNSCs, P3 (S11)


title: 53.1,tumor [DSP-1001660005320-D-D02]


title: 84.3,tumor [DSP-1001660005320-D-C12]


title: qNSCs, P3 (S9)


title: 84.3,stroma [DSP-1001660005320-D-D01]


title: qNSCs, P3 (S8)


title: qNSCs, P3 (S217)


title: 84.1,stroma [DSP-1001660005320-D-C09]


title: 84.2,tumor [DSP-1001660005320-D-C10]


title: 84.2,stroma [DSP-1001660005320-D-C11]


title: 53.3,stroma [DSP-1001660005320-D-D07]


title: qNSCs, P3 (S6)


title: qNSCs, P3 (S7)


title: 73.2,tumor [DSP-1001660005320-D-C06]


title: qNSCs, P3 (S3)


title: 73.2,stroma [DSP-1001660005320-D-C07]


title: 73.1,stroma [DSP-1001660005320-D-C05]


title: qNSCs, P3 (S4)


title: 73.1,tumor [DSP-1001660005320-D-C04]


title: qNSCs, P3 (S5)


title: qNSCs, P3 (S1)


title: qNSCs, P14 (S216)


title: qNSCs, P14 (S215)


title: 10.2,stroma [DSP-1001660005320-D-C03]


title: qNSCs, P14 (S214)


title: 10.1,tumor [DSP-1001660005320-D-B12]


title: 96.2,tumor [DSP-1001660005320-D-B10]


title: qNSCs, P14 (S211)


title: 96.2,stroma [DSP-1001660005320-D-B11]


title: qNSCs, P14 (S210)


title: qNSCs, P14 (S208)


title: 96.1,stroma [DSP-1001660005320-D-B09]


title: 84.1,tumor [DSP-1001660005320-D-C08]


title: 96.1,tumor [DSP-1001660005320-D-B08]


title: qNSCs, P14 (S207)


title: 65.3,stroma [DSP-1001660005320-D-B07]


title: 65.3,tumor [DSP-1001660005320-D-B06]


title: qNSCs, P14 (S205)


title: qNSCs, P3 (S2)


title: qNSCs, P14 (S204)


title: 65.2,stroma [DSP-1001660005320-D-B05]


title: 65.2,tumor [DSP-1001660005320-D-B04]


title: 65.1,stroma [DSP-1001660005320-D-B03]


title: 65.1,tumor [DSP-1001660005320-D-B02]


title: 10.2,tumor [DSP-1001660005320-D-C02]


title: qNSCs, P14 (S203)


title: qNSCs, P14 (S201)


title: qNSCs, P14 (S199)


title: qNSCs, P14 (S213)


title: 10.1,stroma [DSP-1001660005320-D-C01]


title: 51.2,stroma [DSP-1001660005320-D-B01]


title: qNSCs, P14 (S198)


title: qNSCs, P14 (S197)


title: 51.2,tumor [DSP-1001660005320-D-A12]


title: qNSCs, P14 (S196)


title: qNSCs, P14 (S195)


title: 94.2,tumor [DSP-1001660005320-D-A08]


title: qNSCs, P14 (S194)


title: 51.1,tumor [DSP-1001660005320-D-A10]


title: 94.1,stroma [DSP-1001660005320-D-A07]


title: qNSCs, P14 (S206)


title: qNSCs, P14 (S192)


title: 51.1,stroma [DSP-1001660005320-D-A11]


title: qNSCs, P14 (S202)


title: 90.2,stroma [DSP-1001660005320-D-A05]


title: 94.1,tumor [DSP-1001660005320-D-A06]


title: 90.2,tumor [DSP-1001660005320-D-A04]


title: qNSCs, P14 (S187)


title: 90.1,tumor [DSP-1001660005320-D-A02]


title: No Template Control,D [DSP-1001660005320-D-A01]


title: qNSCs, P14 (S186)


title: qNSCs, P14 (S184)


title: qNSCs, P14 (S189)


title: qNSCs, P14 (S183)


title: qNSCs, P14 (S181)


title: qNSCs, P14 (S180)


title: 94.2,stroma [DSP-1001660005320-D-A09]


title: qNSCs, P14 (S193)


title: qNSCs, P14 (S179)


title: DGM-01355_AM

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: alveolar macrophages obtained from bronchoalveolar lavage

data_processing:
Firecrest from Illumina RTA pipeline version 1.6 analyzed images acquired by the Illumina Genome Analyzer II.
Expression analysis was performed using Bowtie (v0.12, http://bowtie-bio.sourceforge.net)
Bowtie default parameters used were those in which the first seed alignment of size > 28 nt, allowing up to 2 mismatches, is chosen at random, and is used if it yields an alignment quality sum of > 70 with a maximum of 125 backtraces.
Resultant reads were aligned (mapped) to the reference genome build UCSC hg19 using Bowtie v 0.12
Bam files of aligned reads from Bowtie were imported into Partek Genomics Suite version 6.5
Aligned reads were mapped to RefSeq gene definition using Partek Genomic Suite.
To correct for transcript length and depth of coverage sequenced reads were converted into reads per kilobase of exon per million fragments sequenced (RPKM).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: gene level rpkm data is a text file exported from Partek Genomics Suite that includes the RPKM values for 8 AM samples.

source_name: alveolar macrophages

extract_protocol:
Total RNA from harvested nonsmoker, smoker and COPD alveolar macrophages was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
Using the reagents of the mRNA Sample Prep Kit and in accordance with the RNA sequencing protocol provided by Illumina, poly(A)+ mRNA was selected out from the total RNA samples using Sera-mag magnetic oligo(dT) beads. An RNA fragmentation kit (Ambion, Austin, TX) was used to fragment the mRNA, followed by first- and second-strand cDNA synthesis using random hexamer primers. An “end repair” reaction to blunt the ends of all fragments was then performed with Klenow polymerase and T4 DNA polymerase, and 3’- to 5’ exo-nuclease was used to create a 3’ adenine overhanging tail, facilitating the ligation of the amplification adapters. Ligation products were then separated on a 2% tris-acetate-EDTA-agarose gel for size selection, followed by purification with a gel extraction kit. The purified ligation products were then PCR amplified with complementary primers and the resultant cDNA was purified with QIAquick PCR kit (Qiagen), and the concentration was measured by the NanoDrop spectrophotometer.
Samples were then loaded onto Illumina flow cells for single end, 43 nucleotide, sequencing reactions
Images acquired by the Illumina Genome Analyzer II were analyzed by Firecrest and bases called by Bustard (both part of Illumina RTA pipeline version 1.6).

tag: smoking status

value: COPD smoker

tag: disease state

value: HIV-

value: alveolar macrophage


title: DGM-10406_AM


title: DGM-00798_AM

value: smoker


title: qNSCs, P14 (S178)


title: DGM-00465_AM

value: nonsmoker


title: DGM-00757_AM


title: DGM-00447_AM


title: qNSCs, P14 (S177)


title: qNSCs, P14 (S190)


title: qNSCs, P14 (S176)


title: qNSCs, P14 (S175)


title: 90.1,stroma [DSP-1001660005320-D-A03]


title: DGM-00262_AM


title: qNSCs, P14 (S188)


title: qNSCs, P14 (S174)


title: qNSCs, P14 (S173)


title: qNSCs, P14 (S172)


title: qNSCs, P14 (S171)


title: qNSCs, P14 (S170)


title: qNSCs, P14 (S169)


title: qNSCs, P14 (S167)


title: DGM-00451_AM


title: qNSCs, P14 (S166)


title: qNSCs, P14 (S168)


title: qNSCs, P14 (S165)


title: qNSCs, P14 (S163)


title: qNSCs, P14 (S164)


title: qNSCs, P14 (S162)


title: qNSCs, P14 (S161)


title: qNSCs, P14 (S160)


title: yolk > sh Ago1 NI [GE1_107_Sep09_2_1_2_R3]

city: STRASBOURG

first: Nicolas

last: MATT

address: 15 rue René Descarte

department: IBMC

country: France

institute: CNRS

description: Gene expression of adult flies knocked down for Ago1 and non immune challenged

hyb_protocol: The resulting Cy3 labeled cRNA was then hybridized onto the 4x44k Drosophila V2 microarray using Agilent GeneExpression Hyb Kit (5188-5242) for 20 hours at 65oC

scan_protocol: The microarray was scanned using Agilent Microarray Scanner (G2565CA) and data extracted with Feature Extraction Software v10.7.2

data_processing:
Median raw expression values where further normalized by quantile method
processed_data_Array_Krupa_22042013_US45103013_252179110070-72.tab
mean over replicates of the four samples and corresponding standard deviation (StD)

organism: Drosophila melanogaster

source_name: adult flies yolk crossed sh-Ago1

label_protocol: Samples were normalized to 100ng in 1.5ul working volume for the labeling reaction and was labeled one-color (Cy3) using Agilent LowInput QuickAmp Labeling Kit (5190-2331)

growth_protocol: Flies were raised on standard cornmeal-yeast-agar medium at 25°C with 60% humidity.

extract_protocol: RNA was extracted from fat bodies and treated with DNAse, using RNA Spin kit (Macherey Nagel). RNA quality was checked by Eukaryote Total RNA Pico assay (Agilent) and validated with a RIN > 6,5. 200 ng of RNA were used to perform micro-array (Agilent DNA microarrays Drosophila).

treatment_protocol: UAS-RNAi flies were crossed with yolk flies at 18°C. Female flies were infected by pricking with Micrococcus luteus (M. luteus). Fat bodies were dissected 4h after infection.

tag: shRNAi

tag: infection

value: Non Induced

tag: slide number

tag: replicat


title: qNSCs, P14 (S159)

tag: tissue

tag: cell type


title: DGM-01774_LA-BC (cross-talk)

description:
DGM-01774
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155379

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using Bowtie (v0.12.8.0, http://bowtie-bio.sourceforge.net), Tophat (v2.0.4, http://tophat.cbcb.umd.edu) and Cufflinks (v2.0.2, http://cufflinks.cbcb.umd.edu).
To correct for transcript length and depth of coverage, raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM) resulting in the fpkm_tracking files.
Resultant fragments were aligned (mapped) to the reference genome build UCSC hg19 using Bowtie.
Non-aligned reads were segmented using Tophat and re-aligned to the genome, aligning reads that span introns and determining junction splice sites. Cufflinks assembled reads into transcripts and assembled reads merged using Cuffmerge; the reads generated from a transcript are directly proportional to the transcripts relative abundance. For the analysis, Tophat (which automatically runs Bowtie) was run for each read pair in a given lane.
For each read pair, Tophat produced one file which contained all reads mapped to the human_g1k_v37 genome and RefSeq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz) transcriptome.
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent Tophat results into one file. This file contains all of the aligned reads for each read pair. Finally, Cufflinks was run on the merged Tophat output to produce a file with FPKM values for each sample.
Data was analyzed using Tuxedo pipeline software.
Genome_build: GRCh37
Supplementary_files_format_and_content: fpkm_tracking files are text files that include the RefSeq gene and location, the FPKM value, high and low confidence and status.

source_name: airway basal cells

growth_protocol: Airway epithelial cells collected by brushing were cultured supplemented with growth factors according to the manufacturer's instructions. Media was changed every 2 days until time of harvest at day 7, when the cells had reached 70 to 80% confluence.

extract_protocol:
Total RNA from harvested nonsmoker and smoker basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA.
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIAquick PCR purification kit (Qiagen, Valencia, CA).
Samples were loaded onto an Illumina flowcell for paired-end 101 x 2 sequencing reactions using the Illumina HiSeq 2000, using a single flow cell with 4 samples multiplexed per lane of flow cell.

value: airway basal cells


title: DGM-10568_LA-BC (cross-talk)

description:
DGM-10568
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155376


title: DGM-10503_LA-BC (cross-talk)

description:
DGM-10503
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155378


title: DGM-10565_LA-BC (cross-talk)

description:
DGM-10565
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155377


title: DGM-10194_LA-BC (cross-talk)

description:
DGM-10194
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155375


title: yolk > sh mCherry M. luteus 4 hrs [GE1_107_Sep09_2_1_3_R2]

description: Gene expression of adult flies knocked down for mCherry and immune challenged by Micrococcus luteus 4 hrs

source_name: adult flies yolk crossed sh-mCherry

value: mCherry

value: Micrococcus luteus innoculated


title: yolk > sh Ago1 NI [GE1_107_Sep09_2_1_2_R2]


title: yolk > sh mCherry NI [GE1_107_Sep09_2_1_1_R3]

description: Gene expression of adult flies knocked down for mCherry and non immune challenged


title: yolk > sh Ago1 M. luteus 4 hrs [GE1_107_Sep09_2_1_4_R2]

description: Gene expression of adult flies knocked down for Ago1 and immune challenged by Micrococcus luteus 4 hrs


title: qNSCs, P14 (S158)

value: Hopx-GFP

value: brain


title: yolk > sh Ago1 M. luteus 4 hrs [GE1_107_Sep09_2_1_4_R3]


title: yolk > sh mCherry M. luteus 4 hrs [GE1_107_Sep09_2_1_3_R1]


title: yolk > sh mCherry NI [GE1_107_Sep09_2_1_1_R2]


title: yolk > sh Ago1 M. luteus 4 hrs [GE1_107_Sep09_2_1_4_R1]


title: yolk > sh Ago1 NI [GE1_107_Sep09_2_1_2_R1]


title: yolk > sh mCherry NI [GE1_107_Sep09_2_1_1_R1]


title: yolk > sh mCherry M. luteus 4 hrs [GE1_107_Sep09_2_1_3_R3]


title: DGM-10284_LA-BC (cross-talk)

description:
DGM-10284
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155374


title: qNSCs, P14 (S156)

value: Dentate Gyrus

value: qNSCs


title: DGM-01657_LA-BC (cross-talk)

description:
DGM-01657
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155373


title: qNSCs, P14 (S153)


title: DGM-11852_LA-BC (cross-talk)

description:
DGM-11852
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155372


title: DGM-01620_LA-BC (cross-talk)

description:
DGM-01620
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155371


title: qNSCs, P14 (S152)


title: qNSCs, P14 (S151)


title: DGM-11374_LA-BC (cross-talk)

description:
DGM-11374
basal cells cultred from airway epithelium samples
Re-accessioned GSM1155370


title: C24 x Col LCM Embryo Rep2

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Reads were first trimmed with trimmomatic
High-quality reads were mapped onto the TAIR10 genome using STAR
Reads overlapping each gene were counted using HTseq with the union and reverse stranded settings
Statistical analysis of differential expression was performed using EdgeR, using linear models to identify differentially expressed genes
Assembly: TAIR10

organism: Arabidopsis thaliana

source_name: Embryo

growth_protocol: Arabidopsis were grown under standard growth room lighting and temperature, with a 16/8 light/dark cycle

extract_protocol:
RNA was isolated from LCM-isolated tissue using the RNAqueous Micro Kit RNA isolation kit
Libraries were prepared using the NEB Ultra II RNA seq kit with poly-A selection module

treatment_protocol: Plants were from controlled crosses, either reciprocal crosses of standrd C24 and Col-0, or from the CNS swpped versions

value: Embryo

tag: genotype

value: C24 x Col


title: qNSCs, P14 (S150)


title: qNSCs, P14 (S149)


title: qNSCs, P14 (S148)


title: qNSCs, P14 (S146)


title: Col x Col LCM Embryo Rep2

value: Col x Col


title: Col x C24 LCM Embryo Rep2

value: Col x C24


title: qNSCs, P14 (S147)


title: C24 x Col LCM Endosperm Rep2

source_name: Endosperm

value: Endosperm


title: Col x C24 LCM Endosperm Rep2


title: qNSCs, P14 (S157)


title: Donor 4 NTHi Day 0

city: St. Lucia

first: Ulrike

last: Kappler

state: Qld

address: Cooper Rd B76

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

description:
D4_NTHi
NTHi_RPKM.txt

data_processing:
CLC Genomics Workbench v 11
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork using default parameters.
Trimmed sequence reads were mapped to using CLC genomic workbench using default settings.
Read count extraction and normalization were performed using CLC genomic workbench
Supplementary files format and content: The procesed data files contains RPKM values for all samples
Supplementary files format and content: tab-delimited text files

organism: Haemophilus influenzae

source_name: bacterial

extract_protocol:
Samples for RNA isolation were collected prior to infection (day0) for uninfected NHNE and bacterial pre-cultures, and on day1, 3, 7 and 14 post-infection for NTHi-infected NHNE. RNA was extracted from 3 replicate NHNE per sample (samples 6-28) or from bacterial cell material collected following growth on BHI agar ( samples 1-5) using TRIZOL (Thermo Fisher), treated with EZDnase to remove remaining gDNA and concentrated usingRNA Clean and Concentrate Kits (Zymo). 2-3 microg total RNA (RIN >8.0) were ribodepleted using the RiboMinus kit (Termo Fisher) and the ribodepleted RNA used for library preparation. For all NHNE samples ~ 70 million reads were collected per sample and mapped to human and NTHi reference genomes. for NTHi infected NHNE samples, approximately 2 milion reads could be mapped to the bacterial genome.
RNA libraries were prepared using the Illumina TruSeq kit

value: bacterial

value: wt

tag: treatment


title: C24 x C24 LCM Endosperm Rep2


title: Col x Col LCM Endosperm Rep2


title: Donor 5 NTHi Day 0

description:
D5_NTHi
NTHi_RPKM.txt


title: Donor 3 NTHi Day 0

description:
D3_NTHi
NTHi_RPKM.txt


title: C24(Col)xCol(C24) LCM CNS Embryo Rep2


title: Col(C24)xCol CNS LCM CNS EmbryoRep2


title: Col(C24) x Col(C24) LCM CNS Embryo Rep2

value: Col(C24) x Col(C24)


title: Donor 1 NTHi Day 0

description:
D1_NTHi
NTHi_RPKM.txt


title: Donor 2 NTHI Day 0

description:
D2_NTHi
NTHi_RPKM.txt


title: C24 x Col LCM Embryo Rep1


title: C24(Col) x C24(Col) LCM CNS Embryo Rep2

value: C24(Col) x C24(Col)


title: Rat 24

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

description: RPI48_S23 -- sample removed from data processing due to poor quality

data_processing:
RNA sequencing data were demultiplexed and trimmed using Partek Flow NGS analysis software (version 10.0.21.0312, St. Louis, MO).
Generated reads were aligned to the rat genome (rn6) using STAR 2.7.3a and raw read counts were normalized by median ratio with DESeq2.
A Storey Q-value cutoff ≤ 0.05 was implemented to identify differentially expressed genes (DEGs).
Assembly: rn6
Supplementary files format and content: tab-delimited text file contains normalized values for each sample

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Frozen lung tissue (~35 mg) was homogenized in TRIzol reagent (ThermoFisher Scientific, Waltham, MA). Total RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research, Irvine, CA) and quantified by a Qubit fluorometer (ThermoFisher Scientific). RNA quality was verified using a Bioanalyzer (Agilent Technologies, Santa Clara, CA). All RNA samples (n =7 – 8 /group) used for sequencing had an RIN ≥ 9.0.
RNA samples (1 µg) were processed on an Apollo324 system (Takara Bio USA, Inc. Mountain View, CA). Notably, one sample from the filtered-air exposed group was removed from further processing due to poor quality. Sequencing libraries were prepared using the PrepX RNA-seq Library Kit for Illumina following the manufacturer’s protocol. Resulting cDNA libraries were amplified by polymerase chain reaction (PCR) with index primers and subsequently assessed using a Qubit and Bioanalyzer. Pooled libraries were diluted to a final concentration of 1.8 pM + 2% PhiX and then sequenced on the NextSeq 500 platform (Illumina Inc., San Diego, CA).

treatment_protocol: To mimic the deployment of common fire line shifts (modified Kelly schedule), rats were exposed to whole-body eucalyptus smoke over the course of two weeks. Exposure occurred for 4 consecutive days on week 1, followed by a 3-day break, and 3 subsequent days of smoke exposure on week 2. Rats (n=24) were randomized by weight into three groups based on body weight (n = 8/group): filtered air, low smoke, and high smoke concentrations. The smoke exposures were set to a target CO concentration of 10 ppm for the low smoke group and 20 ppm for the high smoke group.

value: Lung

value: Male

value: High Smoke


title: Col x C24 LCM Embryo Rep1


title: Rat 23


title: Rat 22


title: Col(C24)xCol LCM CNS Endosperm Rep2

source_name: Endopsperm

value: Endopsperm


title: C24 x C24 LCM Embryo Rep1


title: Rat 21


title: C24 x C24 LCM Embryo Rep2


title: C24(Col)xCol(C24) LCM CNS Endosperm Rep2


title: Rat 17


title: Col x Col LCM Embryo Rep1


title: Rat 20


title: Rat 18


title: C24 x Col LCM Endosperm Rep1


title: Rat 19


title: Col(C24) x Col(C24) LCM CNS Endosperm Rep2


title: Rat 15

value: Low Smoke


title: Rat 16


title: Col x C24 LCM Endosperm Rep1


title: Rat 13


title: Rat 14


title: C24 x C24 LCM Endosperm Rep1


title: KS_II_age_control

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

institute: Westmead Institute of Medical Research

data_processing:
Demultiplexed  sequencing reads were processed using Cell Ranger (v 6.1.1) and mapped to the human reference genome (GRCh38)
Assembly: hg38
Supplementary files format and content: Filtered gene matrices- text

source_name: PBMC

extract_protocol:
Venous blood samples of 4mL were collected in Vacutainer ACD tubes (BD Biosciences) and transferred into 15mL Falcon tubes (Thermo Fisher Scientific). Samples were diluted with 4mL of serum-free wash buffer (PBS (-Ca2+/-Mg2+). 4.5mL of Ficoll Histopaque was added to 15mL SepMate Tubes (Stemcell Technologies). 8mL of diluted blood was gently layered on top of the Ficol Histopaque using auto pipette, ensuring separation of layers. The samples were centrifuged at 1200 x g at room temperature for 15 min. ~1mL of PBMC was aspirated from the interphase between histopaque and the medium and into a 50mL Falcon tube. The remaining supernatant was decanted into the Falcon tube and PBS buffer was added up to 50mL. Samples were washed and centrifuged twice at 250 x g at room temperature for 6 min. The cells were counted. The supernatant was removed without disturbing the pellet, and the pellet was resuspended in 200uL 1X Lysis Buffer with Detergent + 2uL phenylmethylsulfonyl fluoride in ethanol (PMSF). Samples were vortexed for 20 sec and heated at 85°C for 10min in heating block. Samples were transferred to -80°C freezer.
Culture media was prepared using 44mL RPMI (1640 Medium – Thermo Fisher Scientific) and 5mL (10%) fetal bovine serum (FBS – Thermo Fisher Scientific) and 500uL GlutaMAX (Thermo Fisher Scientific). Wash buffer was prepared using Dulbecco’s phosphate-buffered saline (DPBS) and 2% FBS. 10mL of culture media was added to a 15mL Falcon tube. PBMC aliquots were thawed in 37°C water bath and transferred to the Falcon tube with culture media. Samples were centrifuged at 250 x g at room temperature for 10 min and the supernatant was aspirated without disturbing the pellet. Samples were resuspended in 3mL of wash buffer. A 15uL counting aliquot was taken and 10mL of wash buffer was added before centrifugation at 250 x g at room temperature for 10 min. Cells were counted in the sample (using manual hemocytometer. The supernatant was aspirated and cells resuspended in wash buffer such that final concentration was 1 million cells/uL.
PBMCs were sorted into a single cell suspension of live cells using the BD FACSAria™ III Cell Sorter and loaded onto a Chromium Next GEM Chip G (10X Genomics) for a target output of 10,000 cells per sample. Single-cell droplet capture was performed on the Chromium Controller (10X Genomics) and the cDNA library was prepared in accordance with the Chromium Next GEM Single Cell 3’ v3.1 (dual index) protocol
The samples were sequenced by AZENTA Life Sciences (China) on an Illumina HiSeq4000 instrument (2x150 base pair paired end run) for a depth of 20,000 reads per cell

value: PBMC

tag: disorder

value: control


title: Col x Col LCM Endosperm Rep1


title: Rat 10


title: KS_II

value: Kabuki syndrome (KS)


title: Rat 11


title: KS_I_diet12Month


title: Rat 9


title: KS_I_baseline


title: Rat 7

value: Air


title: Rat 6


title: Hippocampus from AppNL-G-F; Lpcat3 f/f, 9 mo; 4306

city: Columbus

first: Jie

last: Gao

state: OH

address: 460 W. 12th Ave

department: The Department of Neuroscience

institute: The Ohio State University

data_processing:
Demultiplexed FASTQ files of bulk RNA sequencing data were aligned to the mouse genome (Mus_musculus.GRCm39) using STAR (version 2.7.10a).
Adapters were trimmed using flexbar (version 3.5.0.).
Reads mapped to genomic features were counted using featureCounts (version 2.0.3).
The count matrix was imported in R (version 4.2.0) for analysis. Gene expression signatures of different experimental conditions were compared using DeSeq2 (version 1.36.0), using the Wald test for hypothesis testing.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Quick-RNA miniprep (R1055, Zymo Research). RNA quality was evaluated by TapeStation using high Sensitivity RNA ScreenTape (5067-5579, Agilent)
RNA seq libraries were prepared using SMART Seq¨ mRNA LP Kit (Takara Bio) following the manufacturerÕs instructions

treatment_protocol: Mice received 20 mg/ml tamoxifen solution via gavage at the dose of  0.2 mg/g body weight

value: Hippocampus

value: WT

tag: gender

value: male

tag: time

value: 9 mo


title: Hippocampus from AppNL-G-F; Lpcat3 f/f; vav1-CRE, 9 mo; 4301

value: Lpcat3 knockout


title: Hippocampus from AppNL-G-F; Lpcat3 f/f, 9 mo; 4307


title: Rat 3


title: C24(Col) x C24(Col) LCM CNS Endosperm Rep2

value: Endosperm


title: Rat 5


title: Rat 4


title: T cells treated with BiTE+sialidase conjugate, replicate 2

city: San Diego

first: Jaroslav

last: Zak

address: 10550 North Torrey Rd

department: Immunology and Microbial Sciences

institute: The Scripps Research Institute

data_processing:
Raw sequencer data were demultiplexed using bcl2fastq by Novogene corporation.
Raw reads in FASTQ formats were aligned to the human genome (GRCh38) with Ensembl v101 transcriptome annotations and gene counts calculated using STAR version 2.7.0f.
Library size normalization of raw reads was performed using DESeq2.
Assembly: GRch38
Supplementary files format and content: Library size-normalized gene counts

source_name: blood

growth_protocol: Human normal donor PBMCs were isolated using standards protocols.

extract_protocol:
CD3+ T cells were isolated using flow cytometry and total RNA isolated using the Picopure RNA isolation kit (Thermo).
polyA+ RNA was subjected to reverse transcription and library generation.

treatment_protocol: 1.2 million hPBMCs and 0.1 million MDA-MB-231 cells were incubated together under the treatment of either 4 nM 4D5 BiTE or 4 nM 4D5 BiTE-sialidase for 48 h.

value: blood

value: T cell

value: wild type

value: 4 nM 4D5 BiTE-sialidase in the presence of MDA-MB-231 cells


title: T cells treated with BiTE+sialidase conjugate, replicate 3


title: Hippocampus from AppNL-G-F; Lpcat3 f/f, 9 mo; 3298


title: Rat 12

value: Lung

value: Male


title: T cells treated with BiTE+sialidase conjugate, replicate 1


title: Hippocampus from AppNL-G-F; Lpcat3 f/f; vav1-CRE, 9 mo; 3300


title: ColxCol(C24) LCM CNS Embryo Rep1

value: Embryo


title: Rat 1


title: Col(C24)xCol LCM CNS Embryo Rep1


title: Hippocampus from AppNL-G-F; Lpcat3 f/f, 9 mo; 3297


title: Col(C24) x Col(C24) LCM CNS Embryo Rep1

value: Col(C24) x Col(C24)


title: Hippocampus from AppNL-G-F; Lpcat3 f/f, 9 mo; 3296


title: KS_I_sibling_control

value: PBMC

value: control


title: ColxCol(C24) LCM CNS Endosperm Rep1


title: Hippocampus from AppNL-G-F; Lpcat3 f/f; vav1-CRE, 9 mo; 3288


title: Col(C24) x Col(C24) LCM CNS Endosperm Rep1


title: T cells treated with BiTE, replicate 3

value: 4 nM 4D5 BiTE in the presence of MDA-MB-231 cells


title: C24(Col) x C24(Col) LCM CNS EndospermRep1

value: C24(Col) x C24(Col)


title: T cells treated with BiTE, replicate 2


title: T cells treated with BiTE, replicate 1


title: Hippocampus from AppNL-G-F; Lpcat3 f/f, 9 mo; 3287

value: Hippocampus

value: WT


title: Hippocampus from AppNL-G-F; Lpcat3 f/f; vav1-CRE, 9 mo; 3286

value: male

value: 9 mo


title: 94664

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
Tophat2 was used to align RNA-seq reads to the human genome
HTSeq was used to quantify gene expression levels
normalization and differential expression analyses were performed by DESeq2
Assembly: hg19
Supplementary files format and content: read counts

source_name: Skin

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus kit
Libraries were constructed from polyadenylated RNA on the Illumina Genome Analyzer Iix

value: Skin

tag: cell line

value: Keratinocyte


title: FH51: Brain, APOE4D

city: Orangeburg

first: Paul

last: Mathews

address: 140 Old Orangeburg Rd.

department: Psychiatry

institute: New York University Grossman School of Medicine

data_processing:
Sequenced reads quality was assessed using Fastqc version 0.11.823 and were trimmed as necessary by Trimmomatic 0.3924. If QC passed and showed no adapter contamination, this step was skipped.
Reads were aligned to the mouse reference genome (Gencode GRCm38-mm10) using STAR Aligner (2.7.0). Aligned reads were quantified using the read summarization algorithm Feature Counts.
The resulting count matrix was tested for differential gene expression using negative binomial generalized regression model from the “DESeq2” package. All genes with fewer than 10 raw read counts across all samples (low expressed genes) were filtered out from the analysis.
P-values were generated by wald test and corrected for multiple testing using the Benjamini and Hochberg false discovery rate (FDR) method.
Assembly: GRCm38-mm10
Supplementary files format and content: EXCEL format; Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Hemibrains were removed, flash frozen on dry ice, and RNA was harvested using the miRNeasy mini kit. Subsequent validation was done for quality and quantity utilizing RNA 6000 Nano kit on the Agilent 2100 bioanalyzer.
RNA-Seq libraries were prepared robotically on a Beckman Biomek Fxp liquid handler using the Illumina TruSeq Stranded mRNA Library Prep kit (catalog # 20020595) starting from 500 ng of total RNA with 10 cycles of final PCR amplification.
All libraries were pooled equimolar and sequenced as Single-read 50 across three lanes of an Illumina HiSeq4000 flowcell.

value: Brain

tag: strain

tag: Sex

value: F

value: 18 months


title: 94665


title: 94663


title: Rat 2

value: Lung

value: Air


title: F19M: Brain, APOE4D

tag: age


title: Col(C24)xCol LCM CNS Endosperm Rep1

value: Endosperm


title: C24(Col) x C24(Col) LCM CNS Embryo Rep1

value: Embryo


title: 94662


title: FH68: Brain, APOE4D


title: FH85: Brain, APOE4D


title: Hippocampus from AppNL-G-F; Lpcat3 f/f; vav1-CRE, 9 mo; 3285

value: Lpcat3 knockout


title: 94658


title: Hippocampus from AppNL-G-F; Lpcat3 f/f; vav1-CRE, 9 mo; 3283


title: 94661


title: 94659


title: 94655


title: 94654


title: Hippocampus from AppNL-G-F; Lpcat3 f/f; vav1-CRE, 9 mo; 3284


title: 94657


title: F12M: Brain, APOE4D


title: FH66: Brain, APOE4


title: 94653

value: TNFa


title: Tumor, Cre+ and Cre-, HTO_Rep2

city: Minneapolis

first: Kathryn

last: Schwertfeger

state: MN

address: 2231 6th St SE

department: Lab Medicine and Pathology

institute: University of Minnesota Medical School

library_source: other

data_processing:
cellRanger v6.0.1: "cellranger count" using cellRanger's built in mouse reference genome
Convert to a seurat object using Read10x() and CreateSeuratObject()
Demultiplex cells using Seurat's HTODemux() function with positive.quantile = 0.8
Filter to Singlet cells with <= 5% MT reads
Normalize counts using SCTransform() with vars.to.regress = "percent_mito"
Assembly: mm10
Supplementary files format and content: CellRanger_metadata_C1C2.tsv contains metadata passed to CellRanger to read in .fastq files
Supplementary files format and content: The three *Counts.tsv files are gene x cell count matrices
Supplementary files format and content: 081_seurat_object.rds is the seurat object used for plotting figures and annotating clusters.

molecule: protein

source_name: Mammary Tumor

extract_protocol:
Tumors were harvested then digested and single cell suspensions were stained for CD45 and viability then FACS sorted. After sorting, each sample was stained with a hashtagging antibody.
Libraries were prepared using the Chromium Single Cell 3’ Library and Reagent Kit v2

value: Mammary Tumor

value: Csf1rfl/fl and Lyve1CreCsf1rfl/fl

value: Flow sorted for CD45

value: CD45+ leukocytes


title: 94656


title: 94652


title: Tumor, Cre+ and Cre-, HTO_Rep1


title: 94649

value: control


title: 94647


title: F95K: Brain, APOE4


title: 94660


title: 94645


title: 94646


title: Tumor, Cre+ and Cre-, GEX_Rep2


title: F58M: Brain, APOE4


title: 94650


title: 94644


title: Tumor, Cre+ and Cre-, GEX_Rep1


title: F64M: Brain, APOE3


title: 94648


title: 94643


title: F10N: Brain, APOE3


title: 94642


title: FH78: Brain, APOE4


title: F78N: Brain, APOE4


title: F37N: Brain, APOE3


title: 94651


title: 94641


title: F39N: Brain, APOE3


title: 351MB_PD1neg, scRNAseq

city: Birmingham

last: Moss

address: University of Birmingham

department: Imunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

description: 10x Genomics

data_processing:
Raw reads were processed using CellRanger (10X Genomics, v5.0.1) functions mkfastq and count. Raw bcl files were converted to fastq and aligned to the human reference genome GRCh38
Assembly: GHch38
Supplementary files format and content: Counts matrix with raw feature counts for each cell.  Rows are genes. Columns are single-cell barcodes (Barcode.1_1 = 297KB PD1 Negative, Barcode.1_2 = 297KB PD1 Positive, Barcode.1.3 = 351MB PD1 Negative, Barcode.1.4 = 351MB PD1 Positive).

growth_protocol: NK cells were quick enriched using negative selection EasySepTM Haman NK cell Enrichment Kit

extract_protocol:
Enriched NK cells were stained with CD56-PE/Cy7, CD3-FITC, PD1-PE, CD19 and CD14-PB and viability dye (flour506-PB) and FACS sorted to obtain pure NK cells higher than 99%.
NK cells were spun down and resuspended in growth media at 1000 cells/ul then sent to Genomics Birmingham-University of Birmingham to check the viability and sequencing . The generated library pool passed the QC in terms of concentration and fragment size as determined using Qubit and TapeStation and was sequenced using a NextSeq 500 (Illumina) platform. The median number of sequenced NK cells returned was 3,500 with 1,500 unique molecular identifiers (UMIs) per cell.Illumina NextSeq 500 (150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.
Illumina NextSeq 500 (150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.

value: PBMC

value: NK Cells

tag: cell subset

value: PD1 Negative NK Cells


title: 94639

value: Skin

value: Keratinocyte


title: F61N: Brain, APOE3

value: Brain

value: F

value: 18 months


title: 94637


title: 94638


title: 94636


title: 297KB_PD1neg, scRNAseq

description: 10x Genomics


title: 351MB_PD1pos, scRNAseq

description: 10x Genomics

value: PD1 positive NK Cells


title: 94634


title: 94633


title: 94632


title: 94635


title: F35J: Brain, APOE2


title: 297KB_PD1pos, scRNAseq

description: 10x Genomics


title: FH111: Brain, APOE2


title: 94631


title: F42N: Brain, APOE2


title: Hu_gingiva_gingivitis_3

city: Richmond

first: Kevin

middle: M

last: Byrd

state: Virginia

address: 521 N 11th St

department: Oral and Craniofacial Molecular Biology

institute: Virginia Commonwealth University

data_processing:
10x Genomics Cell Ranger analytical pipeline v3.1.0
Assembly: GRCh38 v3.0.0
Supplementary files format and content: Features/matrix/barcodes files for raw and processed in .gz.

source_name: Gingiva

extract_protocol:
Split tissues were placed immediately in ice-cold, calcium-free and magnesium-free 1× PBS for overnight shaking and incubation with 1:1,000 ROCK inhibitor (Sigma-Aldrich, Y27632). Cold protease dissociation cocktail was made using cold 1× PBS, 2× DNase (2.5mg ml−1 , Sigma-Aldrich, 9003-98-9) and 1:1,000 ROCK inhibitor. Protease (Sigma-Aldrich, P5380) was then added to a concentration of 100mg ml−1 . Sterilized dissecting forceps (Roboz) were used to mechanically separate gingival into several pieces. The enzymatic cocktail was incubated with gingival tissues for 35min, but progress was checked every 10min with 10-μl aliquots. Dissociation was completed when >75% of the solution was single cells, and then gingival single cells were pelleted at 1,800 relative centrifugal force and washed twice with an appreciable volume of a cocktail of cold culture medium, 1:1,000 Y-27632 and 10% FBS. After dissociation, viability was checked using Trypan blue (viability was confirmed >80%), and red blood cell (RBC) lysis was achieved using a 1× RBC buffer (BioLegend, 420301). A fluorescence-activated cell sorting (FACS) buffer (a mixture of PBS, 1% FBS and 1:1,000 ROCK inhibitor) was used throughout the resuspension and cell sorting process. Single cells were enriched using a 35-mm Falcon cell strainer (Thermo Fisher Scientific). Before FACS, the cell pellet was resuspended in the FACS buffer and stored on ice. To isolate living cells by FACS, rat anti-CD49f Alexa Fluor 647 (a6-Integrin, BioLegend clone GoH3) was added to cells and incubated for 60min on ice. Sytox (Thermo Fisher Scientific, 1:1,000) was added 5min before FACS to evaluate live/dead cells using a Sony SH800S Cell Sorter, with the following controls: anti-CD49f Alexa Fluor 647-negative and Sytox Dead Cell Stain-negative cell suspensions. Cells were sorted ~6 counts per s, and live cells were sorted into tubes directly for 10x capture, library preparation and scRNA-seq.
Gel beads in emulsion (GEMs) were broken, and the complementary DNA (cDNA) libraries were purified using Dynabeads MyOne SILANE (Invitrogen) before 12 amplification cycles. Amplified libraries were purified with SPRIselect magnetic beads (Beckman Coulter) and quantified using an Agilent Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). Fragmentation, end repair, A-tailing and double-sided size selection using SPRIselect beads were then performed. Illumina-compatible adapters were ligated onto the size-selected cDNA fragments. Adapter-ligated cDNA was then purified using SPRIselect beads. Uniquely identifiable indexes were added during 12 amplification cycles. The finalized sequencing libraries were then purified using SPRIselect beads, visualized using the Bioanalyzer High Sensitivity DNA chip, quantified with the KAPA SYBR FAST Universal qPCR Kit for Illumina (Roche) and StepOnePlus Real-Time PCR System (Applied Biosystems), normalized to 4nM and pooled. Pooled libraries were sequenced on a NextSeq 500 machine (Illumina). Libraries were denatured and diluted following standard Illumina protocol, spiked with 1% PhiX sequencing control (Illumina), loaded onto the flow cell at 1.8 pM and sequenced in paired-end format (Read 1: 28bp, Read 2: 91bp) to a total depth of 523million read pairs passing quality filters.
Approximately 3,200 cells per sample were loaded onto the Chromium Chip B with a target recovery of 2,000 cells per sample for library preparation. Single cells, reverse transcription reagents and gel beads coated with barcoded oligos were encapsulated together in an oil droplet to produce gel beads in emulsion (GEMs). Reverse transcription was performed using a C1000 thermal cycler (Bio-Rad) to generate complementary DNA (cDNA) libraries tagged with a cell barcode and unique molecular index (UMI).

value: Gingiva

value: male

value: Molar

tag: subject status

value: gingiva with induced gingivitis

tag: subject race/ethnicity

value: Caucasian


title: Hu_gingiva_gingivitis_4

value: female


title: Hu_gingiva_gingivitis_2

value: African-American


title: Hu_gingiva_gingivitis_1


title: Input_CPT60_rep2

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

data_processing:
library strategy: DRIP-seq
DRIP-seq libraries were quality checked using Fastqc and reads were trimmed using Cutadapt.
Reads were aligned on both human genome (hg 19) and spike-in yeast genome (sacCer3) using BWA aligner.
Alignment sorting, filtering for ENCODE blacklist region and duplicated reads removal was performed using Samtools.
Peak calling and genomic signal computation for each library was performed using macs2.
DRIP-seq signal tracks for each condition were created using Deeptools bamCoverage function, using the normalization scaling factor computed using  library dimension and spike-in fraction for each library.
Assembly: hg19
Supplementary files format and content: .bw file contain the normalized genomic level of DRIP signal
Supplementary files format and content: .narrowPeak file contain the output of MACS peak caller in BED format

growth_protocol: HCT116 cells were cultured in a humidified incubator at 5% of CO2 and 37°C in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (FBS)

extract_protocol:
Cells were harvested by using accutase, pelleted, resuspended in 1X TE buffer (Tris HCl pH 7.6 10 mM, EDTA pH 8 1 mM) and lysed O/N at 37°C with 0.5% SDS and 62.5 μg/ml in 1X TE buffer. Chromatin was then precipited with isopropanolo and sodio acetato, washed with ethanol and resuspeded in 1X TE for 4h at 30°C. O/N digestion was performed with restriction enzymes cocktail
Library construction using the ThruPLEX DNA-Seq kit.

treatment_protocol: HCT116 cells were treated with 10 μM CPT for 5 and 60 minutes.

value: Human epithelial colorectal carcinoma

tag: antibody


title: 94628


title: Input_CPT5_rep2


title: 94627


title: F74M: Brain, APOE2


title: Input_Ctrl_rep2


title: 94626


title: 94625


title: DRIP+RH_CPT60_rep2


title: LuCap35CR_siV7_rep3

city: Boston

first: Maryam

last: Labaf

state: MA

address: 100 William T Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

data_processing:
Raw reads were processed for quality control using fastqc (v.0.11.5)
Raw reads were aligned to Ensembl, GRCh37 using STAR (v2.5.3a)
Gene level read counts was produced by featureCounts from Subread (v1.6.2) package
Assembly: Ensembl GRCH37
Supplementary files format and content: tab-deliminated text files include raw gene counts

growth_protocol: LuCaP35CR cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
TruSeq® Strnd Total RNA LT (Illumina) was used for RNA-Seq library construction.

treatment_protocol: LuCaP35CR cells were grown in 5%CSS and were transfected with siRNAs agaisnt NTC or AR-V7 for 3 days.

value: Prostate Cancer Cell (PDX-derived)


title: 94624


title: 94623


title: LuCap35CR_siV7_rep2


title: DRIP+RH_CPT5_rep2


title: LuCap35CR_siV7_rep1


title: 94621


title: DRIP+RH_Ctrl_rep2


title: 94622


title: 94629


title: 94630

value: control


title: 94618


title: DRIP_CPT5_rep2


title: 94620


title: DRIP_CPT60_rep2


title: LuCap35CR_siNTC_rep2

value: siNTC


title: LuCap35CR_siNTC_rep3


title: 94619

value: Skin


title: 94615

value: Keratinocyte

value: TNFa


title: 94616


title: 94614


title: 94613


title: FH124: Brain, APOE2

value: Brain

value: F


title: LN-Cu-ARv567es_CSS_Cu_rep2

description:
LNCaP_V567_Cu5000_rep2
LN-Cu-ARV567es_count.txt

growth_protocol: LN-tet-ARV7, LN-tet-ARV7-S81A and AR-Cu-ARV567es cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days

treatment_protocol: LN-tet-ARV7, LN-tet-ARV7-S81A and AR-Cu-ARV567es cells were grown in 5%CSS and treated with or without doxycycline for 2 days for AR-V7 transcriptome analyses or cumate for 2 days for AR-V567es transcriptome analyses. CWR-22RV1 cells were transfected with siRNAs agaisnt NTC or AR-V7 for 3 days.

value: Prostate Cancer Cell Line (generated from LNCaP)

value: Cumate


title: MCF7-E2 biol rep 3

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
counts_11_E2
2022-07-30_Annotated_read_counts.csv
Estradiol_3

data_processing:
Reads were aligned using Hisat2 (Version 2.2.1)
Reads were counted using featureCounts program in the Subread (Version 2.0.1) package
Assembly: hg38
Supplementary files format and content: comma separated value (.csv) files containing raw read counts

source_name: Breast

growth_protocol: Phenol red-free DMEM + 10% charcoal-stripped FBS for 3 days

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN). mRNA was selectively isolated from total RNA (1 ug input) using poly-T oligos attached to magnetic beads according to the manufacturer’s guidelines in the NEBNext poly(A) mRNA magnetic isolation module (Cat. #: E7490, NEB, Ipswich, MA).
The library preparation from the enriched mRNA was conducted according to NEBNext Ultra II Directional RNA kit

treatment_protocol: DMSO,  1 nM E2, 100 nM Fulv, or 100 nM Fulv +1 nM E2, for 24 hours

value: Breast

value: Epithelial

value: 1 nM E2


title: 94612


title: MCF7-Fulv+E2 biol rep 3

description:
counts_12_FULV_E2
2022-07-30_Annotated_read_counts.csv
Fulvestrant+Estradiol_3

value: 100 nM Fulvestrant + 1 nM E2


title: 94617


title: LN-Cu-ARv567es_CSS_Cu_rep1

description:
LNCaP_V567_Cu5000_rep1
LN-Cu-ARV567es_count.txt


title: MCF7-Fulv biol rep 3

description:
counts_10_FULV
2022-07-30_Annotated_read_counts.csv
Fulvestrant_3

value: 100 nM Fulvestrant


title: 94608

value: WT


title: 94607


title: 94611


title: LN-Cu-ARv567es_CSS_Veh_rep1

description:
LNCaP_V567_Ctrl_rep1
LN-Cu-ARV567es_count.txt

value: Vehicle


title: LuCap35CR_siNTC_rep1

value: Prostate Cancer Cell (PDX-derived)


title: 94609


title: MCF7-Fulv+E2 biol rep 2

description:
counts_08_FULV_E2
2022-07-30_Annotated_read_counts.csv
Fulvestrant+Estradiol_2


title: LN-Cu-ARv567es_CSS_Veh_rep2

description:
LNCaP_V567_Ctrl_rep2
LN-Cu-ARV567es_count.txt


title: DRIP_Ctrl_rep2

value: Human epithelial colorectal carcinoma


title: 94606


title: 94602


title: 94610


title: 94605


title: 94604


title: 94603


title: MCF7-E2 biol rep 2

description:
counts_07_E2
2022-07-30_Annotated_read_counts.csv
Estradiol_2


title: DGM-13206_Sample_92

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Raw reads from 240 sequenced samples pooled from the 3 healthy, nonsmoker subjects were processed with Salmon to obtain gene and transcript levels as estimated read counts and transcripts per million (TPM) using the Ensembl release 79 transcriptome.
Samples with <10e6 reads or for which less than 80% of fragments mapped to non-mitochondrial protein coding genes were excluded from the final analysis, leaving data from a total of 157 single cells.
For all analyses, TPM values were log transformed as log2(1+TPM). Genes which were not expressed in any sample were excluded, leaving a total of 21,757 genes after filtering. Eighteen samples with no visible cell captured and <10e6 mapped reads (“no cell” wells) were used to estimate background levels of RNA contamination for each gene detected. For 855 genes expressed in at least 20% of no cell wells, background levels were estimated from estimated read counts by fitting an exponential distribution. Estimated read counts for affected genes were corrected by subtracting background levels (to a minimum of 0) and TPM values were recalculated using the corrected read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: log TPM text files include the Ensembl unique ID and gene symbol and log2(1+TPM) values for all samples.

source_name: small airway epithelium brushing

extract_protocol:
Single cell capture, RNA extraction and cDNA preparation were performed on the Fluidigm C1 system following the manufacturer’s protocol. To enrich the cell capture of club cells and basal cells, and minimize the inclusion with larger differentiated ciliated and mucin-secreting cells, the single cell suspension (15 μl; 400~600 cells/μl) were loaded into the medium-sized (10 to 17 μm in diameter) microfluidic RNA-seq chip after priming (Fluidigm). The cells were captured using an Olympus-phase contrast microscope to examine the cell numbers in each capture site. Only single cells in the capture site were used.
The Fluidigm C1 system was used for single cell RNA purification and cDNA synthesis by using the SMARTer Ultra Low RNA kit, and the single cell cDNAs were transferred to a 96 well-plate. The single cell library preparation and RNA sequencing were performed following a Fluidigm protocol.
The single cell libraries were pooled and sequenced with paired end clustering and 101x2 cycles sequencing on the Illumina Hiseq 2500

tag: individual id

tag: smoking status

value: nonsmoker

value: SAE


title: DGM-13206_Sample_91


title: 94598

tag: tissue

value: Skin

value: Keratinocyte


title: 94600

tag: cell type


title: 94601


title: MCF7-Veh biol rep 3

description:
counts_09_DMSO
2022-07-30_Annotated_read_counts.csv
Vehicle_3

value: DMSO


title: 94596

value: control


title: DGM-13206_Sample_9


title: MCF7-Fulv biol rep 1

description:
counts_02_FULV
2022-07-30_Annotated_read_counts.csv
Fulvestrant_1


title: 94599

value: TNFa


title: 94594


title: DGM-13206_Sample_89


title: MCF7-Fulv+E2 biol rep 1

description:
counts_04_FULV_E2
2022-07-30_Annotated_read_counts.csv
Fulvestrant+Estradiol_1


title: D2-KO_2

city: Chicago

first: Joseph

middle: G

last: O'Brien

state: IL

address: 445 E Ohio St, Apt 1818

department: Genetics

institute: Northwestern

data_processing:
Sequences were trimmed for adapter sequence based on quality of the reads using fastqc/0.11.5
Trimmed sequences were aligned to the mm10 reference genome using tophat/2.1.0
Read count extraction and normalization was gathered using Bioconductor edgeR open source software
Assembly: mm10
Supplementary files format and content: Tab-deliminated text file includes raw counts for each sample
Supplementary files format and content: Tab-deliminated text file includes CPM values for each sample

source_name: Quadriceps

growth_protocol: 3 Female mice per cohort, aged 16 weeks

extract_protocol:
RNA was extracted from whole quadriceps using TRIzol and filted with Aurum Total RNA Mini-kit. RNA was suspended in 30ul of RNase-Free Water
The Illumina RNA Sample Prep Kit version 2.0 generated libraries and aligned to the mm10 reference

value: Quadriceps

value: Female

value: 16 weeks

tag: genotype


title: 94597

tag: treatment


title: MCF7-Fulv biol rep 2

description:
counts_06_FULV
2022-07-30_Annotated_read_counts.csv
Fulvestrant_2

value: Breast

value: Epithelial


title: MCF7-E2 biol rep 1

description:
counts_03_E2
2022-07-30_Annotated_read_counts.csv
Estradiol_1

value: 1 nM E2


title: DGM-13206_Sample_86

city: New York

last: Strulovici-Barel

address: 1300 York Avenue

institute: Weill Cornell Medical College


title: MCF7-Veh biol rep 2

description:
counts_05_DMSO
2022-07-30_Annotated_read_counts.csv
Vehicle_2


title: DGM-13206_Sample_85


title: D2-KO_3


title: DGM-13206_Sample_87


title: D2-WT_1


title: D2-KO_1


title: D2-WT_3


title: DGM-13206_Sample_78


title: 94640


title: MRL-WT_3


title: MRL-WT_2


title: DGM-13206_Sample_80