title: 10 day thorax Sirt6-/- biol rep 4

city: Cleveland

first: Jackson

last: Taylor

state: Ohio

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences

institute: Cleveland State University

description:
Library name: t.s6ko.4
R24

data_processing:
STAR 2.7.11b Aligner - BAM sorted by coordinate
Subread 2.0.8 - featureCounts - paired - unstranded
Normalized raw counts with DESeq2 by tissue
Assembly: dm6 - NCBI RefSeq assembly - GCF_000001215.4 - Genome assembly Release 6 plus ISO1 MT
Supplementary files format and content: raw_counts.csv.gz - Raw counts from all samples from featureCounts
Supplementary files format and content: normalized_counts.csv.gz - All samples normalized by tissue with DESeq2

organism: Drosophila melanogaster

source_name: Thorax

growth_protocol: Flies were collected within 24 hours of eclosion and aged for 10 days while maintained on 15% dextrose/15% yeast/2% agar food at 25 °C on a 12-h light/dark cycle at 60% relative humidity. Food was changed every two days.

extract_protocol:
Zymo Direct-zol Micro
Poly A Selection (by Azenta/Genewiz)

treatment_protocol: Sirt6 -/- line was made by deleting part of exon 1, including start codon, using CRISPR (see PMC8920434). Control line is w1118 backcrossed eight generations to Sirt6-/- line.

value: Thorax

value: Male

value: 10 day

value: Sirt6 -/-

value: Sirt6 deletion


title: D52_R1_NSC

status: Public on Jul 06 2026

type: SRA

city: Oxford

first: Nick

last: Gatford

address: Dorothy Crowfoot Hodgkin Building, South Parks Road

department: NDCN

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Paired end files (150 bp) were generated for each sample
Kallisto (v0.46.2) was used to estimate transcript abundance for Ensembl (release 102) protein-coding genes from RNAseq reads
Count data was imported into R using tximport and genes with less than 10 reads across the six samples used in the comparison were filtered out
Differential gene expression was performed in DESeq2 using the Wald test with an FDR threshold of 0.05 and a log2 fold change threshold on 0.25
Assembly: GRCh38 (Ensemble release 102)
Supplementary files format and content: Kallisto quantification files (tsv files and HDF5 binary files) for each sample with run info, transcript abundance estimates, TPM, bootstrap estimates, and transcript length information length

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: iPSC differentiation into dopaminergic neurons to DIV 52 or DIV 60

extract_protocol:
RNeasy Plus Mini Kit, Qiagen (Cat No./ID: 74134)
Library preparation was performed with the NEB Next Ultra RNA Library Prep Kit, following standard Illumina protocols. Libraries were sequenced with NovaSeq 6000 (Illumina).
Unstranded library, poly-A enriched RNA-Seq

treatment_protocol: NSC

tag: cell line

tag: cell type

value: Induced pluripotent stem cell derived dopaminergic neurons

tag: treatment

value: NSC

tag: time

value: day 52


title: 10 day thorax Sirt6-/- biol rep 3

country: USA

description:
Library name: t.s6ko.3
R23

molecule: total RNA

tag: tissue

tag: Sex

tag: age

tag: genotype

tag: batch


title: 10 day thorax Sirt6-/- biol rep 2

description:
Library name: t.s6ko.2
R22


title: 10 day thorax Sirt6-/- biol rep 1

description:
Library name: t.s6ko.1
R21


title: 10 day thorax wild type biol rep 3

description:
Library name: t.wt.3
R19

value: Control


title: 10 day thorax wild type biol rep 2

description:
Library name: t.wt.2
R18


title: 10 day thorax wild type biol rep 4

description:
Library name: t.wt.4
R20


title: 10 day abdomen Sirt6-/- biol rep 4

description:
Library name: a.s6ko.4
R16

source_name: Eviscerated Abdomen

value: Eviscerated Abdomen


title: 10 day abdomen Sirt6-/- biol rep 3

description:
Library name: a.s6ko.3
R15


title: 10 day abdomen Sirt6-/- biol rep 1

description:
Library name: a.s6ko.1
R13


title: 10 day abdomen Sirt6-/- biol rep 2

description:
Library name: a.s6ko.2
R14


title: 10 day abdomen wild type biol rep 4

description:
Library name: a.wt.4
R12


title: 10 day abdomen wild type biol rep 3

description:
Library name: a.wt.3
R11


title: 10 day abdomen wild type biol rep 2

description:
Library name: a.wt.2
R10


title: 10 day abdomen wild type biol rep 1

description:
Library name: a.wt.1
R9


title: 10 day head Sirt6-/- biol rep 4

description:
Library name: h.s6ko.4
R8

source_name: Head

value: Head


title: 10 day head Sirt6-/- biol rep 3

description:
Library name: h.s6ko.3
R7


title: 10 day head Sirt6-/- biol rep 2

description:
Library name: h.s6ko.2
R6


title: 10 day head Sirt6-/- biol rep 1

description:
Library name: h.s6ko.1
R5


title: 10 day head wild type biol rep 3

description:
Library name: h.wt.3
R3


title: 10 day head wild type biol rep 2

description:
Library name: h.wt.2
R2


title: 10 day head wild type biol rep 1

description:
Library name: h.wt.1
R1

value: Control Male 10d


title: CAR5p_CD22_RPMI8226_hashing

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: Library name: CAR5p_CD22_RPMI8226_hashing

data_processing:
Raw Aviti .bases files were demultiplexed with Bases2Fastq v2.2
Gene expression reads were aligned to the human hg38 reference genome with CellRanger v8.0.0
Hashing data was pseudoaligned to a hash tag oligo reference using kallisto v0.44 and processed into counts matrices with bustools v0.7
Cell x gene counts matrices in h5 format were produced using the default parameters in CellRanger count
Assembly: hg38
Supplementary files format and content: Gene expression counts matrices (h5) from CellRanger pipeline
Supplementary files format and content: Hash assignments from Seurat v5 HTO demux

source_name: primary CAR T cells

growth_protocol: T cells were isolated from Stem Cell Leukopacks (Stem Cell, Cat. 200-0092) using EasySep Human T Cell Isolation Kit (Stem Cell, Cat. 17951). Upon thawing, cells (Day 2) were resuspended in Immunocult (Stem Cell, Cat. 10981) supplemented with 0.1ug/mL of IL-2 (Stem Cell, Cat. 78036) and activated with ImmunoCult Human CD3/CD28 T Cell Activator (Stem Cell, Cat. 10971). Cells were maintained at a concentration of 0.25e6/mL. On Day 2, concentrated lentivirus was added to cells, and cells were spin-infected at 800g for 45 minutes. On Day 5, DAPI-stained T cells were sorted for GFP+ cells using the SH800S Cell Sorter.

extract_protocol: 10x Genomics NextGEM 5' scRNA-seq

treatment_protocol: Cells were stimulated with co-cultures of noted cell lines and profiled 24 hours later

value: primary CAR T cells

tag: cell line_co-culture


title: CAR5p_CD22_RPMI8226_GEX

description: Library name: CAR5p_CD22_RPMI8226_GEX

library_source: transcriptomic single cell


title: CAR5p_BCMA_hashing

description: Library name: CAR5p_BCMA_hashing


title: CAR5p_BCMA_GEX

description: Library name: CAR5p_BCMA_GEX


title: CAR5p_CD22_K562OE_GEX

description: Library name: CAR5p_CD22_K562OE_GEX


title: CAOV3 cells, shMT2A shRNA2, replicate 4

city: Charleston

first: Joe

middle: R

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description: Library name: CAOV3_shMT2A-2_12

data_processing:
STAR alignment to hg38, featureCounts for transcript read counts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: tumor

growth_protocol: Live cells were kept in a 37 °C air-jacketed tissue culture incubator (VWR, #10810-902, Radnor, PA, USA) with 5% CO2. All assays utilized RPMI-1640 1× with L-Glutamine media (Corning, #10040CV, Glendale, AZ, USA) supplemented with 10% fetal bovine serum (Gibco, #A5256701, Waltham, MA, USA), 1% sodium pyruvate (Sigma-Aldrich, #S8636, St. Louis, MO, USA), and 1% penicillin streptomycin (Gibco, #15140122). CAOV3 cells (ATCC, #HTB-75, Manassas, VA, USA) were transduced with either shScr (pLKO.1, Addgene #1864, Watertown, MA, USA), shMT2A-1 (TRCN0000148975, Sigma-Aldrich, targeting sequence GCAAAGAGTGCAAATGCACTT), or shMT2A-2 (TRCN0000148783, Sigma-Aldrich, targeting sequence CTGCAAATGCAAAGAGTGCAA). CAOV3 cells were derived from the ovary of a 54-year-old female ovarian cancer patient and are morphologically epithelial.

extract_protocol:
Invitrogen PureLink RNA mini kit (12183018A)
NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (NEB#E7490), polyA mRNA workflow

treatment_protocol: normal growth

value: tumor

value: ovarian cancer cells

value: MT2A knockdown2


title: CAOV3 cells, shMT2A shRNA2, replicate 3

description: Library name: CAOV3_shMT2A-2_9


title: CAOV3 cells, shMT2A shRNA2, replicate 2

description: Library name: CAOV3_shMT2A-2_6


title: CAOV3 cells, shMT2A shRNA2, replicate 1

description: Library name: CAOV3_shMT2A-2_3


title: CAOV3 cells, shMT2A shRNA1, replicate 3

description: Library name: CAOV3_shMT2A-1_11

value: MT2A knockdown1


title: CAOV3 cells, shMT2A shRNA1, replicate 2

description: Library name: CAOV3_shMT2A-1_5


title: CAOV3 cells, shMT2A shRNA1, replicate 1

description: Library name: CAOV3_shMT2A-1_2


title: CAOV3 cells, shScrambled control, replicate 4

description: Library name: CAOV3_shScr_10

value: control


title: CAOV3 cells, shScrambled control, replicate 3

description: Library name: CAOV3_shScr_7


title: CAOV3 cells, shScrambled control, replicate 2

description: Library name: CAOV3_shScr_4


title: Ax2 growth with S. mutans - replicate 1

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Library name: Ax2M1

data_processing:
Paired-end reads were trimmed for sequencing adapters using Trimmomatic v0.38 with parameters LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36.
Trimmed reads were aligned with HISAT2 v2.2.1 with options -dta and --rna-strandness=RF against the reference Dictyostelium AX4 genome
Quantification of the Dictyostelium AX4 transcript expression (reference: AX4_GCF_000004695.1) was performed with StringTie v2.1.3b
Differential expression analysis was performed with DESeq2 v1.52 with default parameters, considering the raw read count table generated by StringTie.
Assembly: Ax2
Supplementary files format and content: Tab-delmited file reporting the raw read count

organism: Dictyostelium discoideum

growth_protocol: Dictyostelium discoideum Ax2 cells were grown in suspension in axenic medium at 23°C at 150 rpm in in a climatic cabinet equipped with gyratory shakers.

extract_protocol:
RNA was extracted with Rneasy kit (Qiagen) according to manufacturer's procedure.
RNA-Seq library preparation was performed using the Illumina TruSeq RNA library.

treatment_protocol: Dictyostelium discoideum Ax2 cells were grown in suspension in Soerensen buffer with E. coli B/r, S. salivarius 24SMBc and S. mutans as the only source of food, at 23°C under shaking at 180 rpm in a climatic cabinet equipped with gyratory shakers for 3 days.

value: amoeba cells

value: Growth with S. mutans


title: Ax2 growth with S. mutans - replicate 3

description: Library name: Ax2M3


title: CAOV3 cells, shScrambled control, replicate 1

description: Library name: CAOV3_shScr_1


title: Ax2 growth with S. salivarius - replicate 2

description: Library name: Ax2S2

value: Growth with S. salivarius


title: Ax2 growth with S. mutans - replicate 2

description: Library name: Ax2M2


title: Ax2 growth with S. salivarius - replicate 1

description: Library name: Ax2S1


title: Ax2 growth with S. salivarius - replicate 3

description: Library name: Ax2S3


title: Ax2 growth with E. coli - replicate 3

description: Library name: Ax2E3

value: Growth with E. coli


title: Ax2 growth with E. coli - replicate 2

description: Library name: Ax2E2


title: CAR5p_CD22_K562OE_hashing

description: Library name: CAR5p_CD22_K562OE_hashing


title: Ax2 growth with E. coli - replicate 1

description: Library name: Ax2E1


title: hTSC CT27, shDNMT1_B, hTSC, Rep 2

city: Philadelphia

first: Sanam

last: Kavari

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Library name: hTSC shDNMT1_B Rep 2

data_processing:
Reads were first trimmed of adaptor sequences and low-quality bases using the trim-galore package (v0.6.11).
Sequencing quality was assessed by FastQC (v0.12.1)
Reads were then aligned and methylation values extracted using Bismark (v0.25.1).
Assembly: hg38
Supplementary files format and content: Coverage files (.cov) have six columns: chromosome, start, stop, % methylation, number of methylated reads, number of unmethylated reads

source_name: Placenta

growth_protocol: hTSCs were cultured in human TSC medium (TSCM), composed of a basal medium (DMEM/F12 supplemented with 1% ITS-X, 0.3% BSA, 0.5X penicillin-streptomycin, 0.2 mM L-ascorbic acid) supplemented with 5 μM A83-01, 2 μM CHIR99021, 25 ng/mL EGF, 2.5 μM Y27632, and 0.8 mM VPA. Cells were cultured at 37°C, 5% CO2, and ambient O2, and the medium was changed or cells were passagedevery 2 days.

extract_protocol:
shRNA transduced hTSCs were collected in cell pellets and frozen at -80C. Pellets were then thawed on ice, and DNA was extracted using the QIAamp DNA Mini Kit. Residual RNA was removed by treatment with 10 μg/mL RNAse at 37 °C for 5 minutes, followed by clean-up of genomic DNA with the QIAamp DNA Micro Kit.
200ng of purified DNA per sample was then subjected to bisulfite conversion with the EpiTect Bisulfite Kit, followed by secondary strand synthesis, tagmentation, and library amplification and purification using the Zymo-Seq WGBS Library Kit and the Illumina Nextera DNA Flex Library Prep Kit. Library size was analyzed by Agilent TapeStation D1000 ScreenTape Assay and quantified by qPCR using the KAPA Library Quantification Kit. Libraries were then sequenced on an Illumina MiSeq i100 with 300bp paired end reads at a depth of 500,000 to 1 million reads per sample.

treatment_protocol: Cells were transduced with lentivirus containing an shRNA targeting DNMT1 or a control, non-targeting shRNA. Two days after transduction, cells were selected in 1 ug/mL puromycin in hTSC media for 4 days. For undifferentiated conditions, cells were maintained in hTSC media with puromycin until 13 days post-transduction..

value: Placenta

value: hTSC CT27

value: human trophoblast stem cell

value: DNMT1 knockdown

value: Undifferentiated hTSC


title: hTSC CT27, shDNMT1_B, hTSC, Rep 3

description: Library name: hTSC shDNMT1_B Rep 3


title: hTSC CT27, shDNMT1_B, hTSC, Rep 1

description: Library name: hTSC shDNMT1_B Rep 1


title: hTSC CT27, shDNMT1_A, hTSC, Rep 1

description: Library name: hTSC shDNMT1_A Rep 1


title: hTSC CT27, shControl, hTSC, Rep 3

description: Library name: hTSC shControl Rep 3


title: hTSC CT27, shDNMT1_A, hTSC, Rep 3

description: Library name: hTSC shDNMT1_A Rep 3


title: hTSC CT27, shControl, hTSC, Rep 2

description: Library name: hTSC shControl Rep 2


title: hTSC CT27, shControl, hTSC, Rep 1

description: Library name: hTSC shControl Rep 1


title: hTSC CT27, shDNMT1_A, hTSC, Rep 2

description: Library name: hTSC shDNMT1_A Rep 2


title: PAO1-WT-1-lane20

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
WT control for  PA0311  PA0338  PA0354  PA0358  PA0389  PA0484  PA0522  PA0526  PA0541  PA0543  PA0553  PA0585  PA0670  PA0977  PA1471  PA1677  PA2380  PA2418  PA2434  PA2436  PA2450  PA2464  PA2471  PA2483  PA2490  PA2764  PA2769  PA2791  PA2792  PA2829  PA2833  PA2860  PA3203  PA3205  PA3219  PA3222  PA3230  PA3233  PA3235  PA3237  PA3258  PA4703  PA5033
NA

data_processing:
RNA-seq reads were mapped to the Pseudomonas aeruginosa (NC_002516.2) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Assembly: Pseudomonas aeruginosa (NC_002516.2)
Supplementary files format and content: xlsx files were generated from RNA-seq, containing the differential expressional genes.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: RNA-seq(LB)

extract_protocol:
The Pseudomonas aeruginosa PAO1 wild type strain and the HP mutants were inoculated into LB with corresponding antibiotics overnight cultured at 37 °C. Then the strains were one hundred times diluted into fresh LB. Before harvested, the P. aeruginosa strains were cultured for 3 h until OD600 to 0.6, at 37 °C with 220 rpm shaking. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4 °C). RNA extraction was performed by using the TianGen RNA extraction kit with the recommended DNase digestion. After removing rRNA by following the RiboRid protocol, mRNA was used to construct the cDNA library according to the NEBNext Ultra II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina).
NEBNext UltraTM II RNA Library Prep Kit protocol

treatment_protocol: grow until mid-log phase

value: Pseudomonas aeruginosa PAO1

value: WT

value: grow until mid-log phase in LB


title: PAO1-WT-1-lane25

description:
WT control for  PA0057  PA0116  PA0135  PA0267  PA0462  PA0556  PA0855  PA1499  PA1522  PA1860  PA2618  PA2179 80  PA2328  PA2487  PA2660 61  PA2695  PA2847  PA2927  PA3012  PA3208 09  PA3216  PA3301 02  PA3304  PA3451  PA3472  PA3564  PA3616  PA3661  PA3726  PA3727 28  PA3762  PA4071  PA4093  PA4095  PA4099  PA4111  PA4121  PA4327 28  PA4360  PA4383  PA4467  PA4573  PA4630  PA4863 68  PA5027  PA5061
NA


title: PAO1-WT-1-lane24

description:
WT control for  PA0038  PA0052  PA0104  PA0112  PA0200  PA0278  PA0469  PA0474  PA0560  PA0566  PA0624  PA0702  PA0777  PA0827  PA0832  PA0856  PA0868  PA0925 26  PA0955  PA0983  PA0988  PA1065  PA1134  PA1291  PA1369  PA1472  PA1492  PA1643  PA1829  PA1830  PA1926  PA1981  PA2095  PA2167  PA2207 09  PA2474  PA2485  PA2544  PA2627 28  PA2682  PA2793  PA2807  PA2880  PA3207  PA3218  PA3325  PA3359  PA3612  PA3698  PA3756  PA3964  PA3967  PA3998  PA4128  PA4485 86  PA4509 11  PA4577  PA4689  PA4075  PA4712
NA


title: PAO1-WT-1-lane23

description:
WT control for  PA0578  PA0636  PA0653  PA0790  PA0894  PA1037  PA1045  PA1143  PA1641  PA2029  PA2156 57  PA2197 98  PA2201  PA2375  PA2428  PA2916  PA2954  PA3015  PA3017  PA3052  PA3079  PA3273  PA3412  PA3819  PA3893  PA4140  PA4421  PA4963
NA


title: PAO1-WT-1-lane22

description:
WT control for  PA0021  PA0069  PA0319  PA0572  PA0614  PA0663  PA0834  PA1112  PA1467  PA1835  PA1934  PA1935  PA2004  PA2037  PA2139  PA2163  PA2433  PA2751  PA2753  PA2756  PA2878  PA2946  PA3125  PA3224  PA3323  PA3734  PA3928  PA3939  PA4570  PA4642 44  PA4851  PA4933  PA5026
NA


title: PAO1-WT-1-lane21

description:
WT control for  PA0013  PA0014  PA0027  PA0042  PA0046  PA0050  PA0064  PA0107  PA0115  PA0118  PA0121  PA0127  PA0144  PA0165  PA0187  PA0250  PA0252  PA0257  PA0264  PA0308  PA0312  PA0332  PA0339  PA0340  PA0343  PA0360  PA0368  PA0377  PA0384  PA0391  PA0418  PA0421  PA0434  PA0442  PA0449  PA0453  PA0457  PA0536  PA0554  PA0557  PA0559  PA1733  PA1872 73  PA4181 82  PA4317 23  PA4495
NA


title: PAO1-WT-1-lane19

description:
WT control for  PA0404  PA0431  PA0433  PA0732  PA0769  PA0841  PA0976  PA1052  PA1152  PA1154  PA1167  PA1186  PA1189  PA1331  PA1358  PA1368  PA1495  PA1547 48  PA1673  PA1729  PA1940  PA1960  PA1967  PA1970  PA2017  PA2027  PA2089 91  PA2166  PA2268  PA2372  PA2502  PA2720  PA2759  PA2770  PA2844  PA2854 55  PA2864  PA3089  PA3318  PA3465  PA3592  PA3605  PA3783  PA3869  PA3955 56  PA4035  PA4368 69  PA4377  PA4620  PA4713  PA4834 36  PA4882 84
NA


title: PAO1-WT-1-lane17

description:
WT control for  PA0047  PA0348  PA0485  PA0498  PA0742  PA0749  PA0820  PA1016  PA1293  PA1625  PA1730  PA2437 39  PA2503  PA2575  PA2576  PA2581  PA2589 90  PA2613  PA2625  PA2668  PA2699  PA2705 07  PA2729  PA2806  PA3240  PA3241  PA3259  PA3270  PA3289  PA3306 07  PA3317  PA3322  PA3335  PA3372 73  PA3374  PA3390  PA3422  PA3436  PA3453  PA3489  PA3496  PA3681  PA3705  PA3730  PA3752 54  PA3755  PA4617  PA4623  PA4870  PA4875
NA


title: PAO1-WT-1-lane18

description:
WT control for  PA0015  PA0043  PA2501  PA2568  PA2602  PA2752  PA2805  PA2817  PA2819  PA2869  PA3403  PA3431 32  PA3444  PA3445  PA3449  PA3497  PA3532  PA3575  PA3613  PA3614  PA3618  PA3662  PA3674  PA3688  PA3786  PA3787 88  PA3941  PA3959 60  PA4586  PA4603 06  PA4618  PA4627  PA4637  PA4657  PA4701  PA4702  PA4711  PA4716  PA4717  PA4718  PA4721  PA4753  PA4782 83  PA4792  PA4802  PA4815  PA4818 20  PA4828  PA4830  PA4926 27  PA4929
NA


title: PAO1-WT-1-lane15

description:
WT control for  PA0646  PA0731  PA0808  PA0902  PA0914  PA0921  PA0924  PA0946  PA1026  PA1139  PA1357  PA1366  PA1411  PA1672  PA1751  PA1824  PA1879  PA2074  PA2141  PA2145  PA2183 84  PA2211 12  PA2311  PA2377  PA2415  PA2484  PA2504  PA2562  PA2757  PA2871  PA3140  PA3320  PA3358  PA3362  PA3435  PA3615  PA3750  PA3764  PA3836  PA3966  PA4076  PA4146  PA4163 64  PA4440  PA5028  PA4515 16
NA


title: PAO1-WT-1-lane16

description:
WT control for  PA0741  PA0758  PA1044  PA1088  PA1135  PA1181  PA1191  PA1195  PA1209  PA1378  PA1381  PA1506  PA1620  PA1640  PA1644  PA2178  PA2440 41  PA2451 52  PA2496  PA2569  PA2595 96  PA2609  PA2650  PA2736  PA3231  PA3255  PA3281 84  PA3287  PA3313  PA3539  PA3572  PA3578  PA3765  PA3772 73  PA3791  PA3892  PA4010 11  PA4015  PA4017  PA4028  PA4038 40  PA4045 46  PA4065 66  PA4087  PA4840  PA4849
NA


title: PAO1-WT-1-lane14

description:
WT control for  PA1118  PA1133  PA1149  PA1355 56  PA1414  PA1559  PA1645  PA1755  PA1769  PA1842  PA1855  PA1909  PA1929  PA1939  PA1942  PA1944  PA1965  PA1966  PA1974  PA2063  PA2221  PA2222 23  PA2326  PA2345  PA2353  PA2457  PA2610  PA2651  PA2658 59  PA2691  PA2784 85  PA2820  PA2884  PA2910
NA


title: 10 day thorax wild type biol rep 1

description:
Library name: t.wt.1
R17

value: Thorax

value: Male

value: 10 day

value: Control


title: PAO1-WT-1-lane13

description:
WT control for  PA0054  PA0061  PA0806  PA0875  PA0891  PA0916  PA1053  PA1937 38  PA1968 69  PA2021  PA2116  PA2175 76  PA2189  PA2309 10  PA2549  PA2582  PA2662  PA3370 71  PA3457  PA3631 32  PA3669 70  PA3675  PA3712  PA3808  PA3979  PA4009  PA4058 60  PA4154  PA4169  PA4335 36  PA4632  PA4833  PA4879
NA


title: PAO1-WT-1-lane12

description:
WT control for  PA0145  PA0251  PA0429  PA0488  PA0542  PA0850  PA0858 59  PA2883  PA1111  PA1116  PA1117  PA1168  PA1230  PA1280  PA1352  PA1607  PA2137  PA2148 50  PA2154  PA2170  PA2186  PA2192  PA2763  PA2773  PA2789  PA2790  PA3849  PA4041  PA4173  PA4535 37  PA4738 39  PA4908
NA


title: PAO1-WT-1-lane10

description:
WT control for  PA0714  PA0878  PA0943  PA1132  PA1401  PA1639  PA1851  PA1865  PA1915 18  PA1943  PA2026  PA2151  PA2171 73  PA2174  PA2181  PA2182  PA2190  PA2205  PA2218  PA2251  PA2264  PA2269  PA2282 87  PA2289  PA2296  PA2346 49  PA2360 64  PA2422  PA2594  PA2761  PA2772  PA2831  PA3031  PA3179  PA3298  PA3826  PA3856  PA3931  PA4324  PA4364  PA4458  PA4580  PA4779
NA


title: PAO1-WT-1-lane11

description:
WT control for  PA0276  PA0284  PA0359  PA0379  PA0486  PA0492  PA0549  PA0589  PA0591  PA0805  PA0813  PA0851  PA0957  PA0989  PA1042  PA1060  PA1069  PA1115  PA1140  PA1188  PA1305 08  PA1408  PA1415  PA1539  PA1575  PA1593  PA1652  PA1734  PA1741  PA2044  PA2066  PA2106  PA2134  PA2630  PA2868  PA3180  PA3342  PA4291  PA4388  PA4441  PA4445  PA4952
NA


title: PAO1-WT-1-lane9

description:
WT control for  PA0392  PA0666  PA0862  PA1005  PA1383  PA1387  PA1398  PA1404  PA1406 07  PA1426  PA1450 51  PA1466  PA1577  PA1606  PA1616  PA2481  PA2737  PA2803 04  PA3367  PA3428  PA3464  PA3623  PA3707  PA3733  PA3850 52  PA3991  PA3944  PA3985 86  PA4132  PA4139  PA4177  PA4746  PA4773  PA4793 96  PA4881  PA4925
NA


title: PAO1-WT-1-lane8

description:
WT control for  PA0049  PA0244  PA0307  PA0309  PA0446  PA0529  PA0539  PA0563  PA0596  PA0788  PA1006  PA1093  PA1095  PA1530  PA1550  PA1578  PA1746  PA1788  PA1849  PA2075  PA2228  PA2229 30  PA2318  PA2430  PA2697  PA3016  PA3199 00  PA3350  PA3352  PA3421  PA4463 65  PA4607  PA4691 92
NA


title: PAO1-WT-1-lane7

description:
WT control for  PA0007  PA0285  PA0734  PA0751  PA0812  PA0959  PA1203  PA1478  PA1605  PA1914  PA1972  PA5024  PA4852  PA4540 41  PA4118  PA4018  PA3919  PA3911  PA3600 01  PA3580  PA2845  PA2768  PA2713  PA2669 71  PA2604  PA2597 00  PA2431  PA0128  PA0277  PA0497  PA0729  PA0874  PA0922  PA0968  PA1011  PA1198  PA1211  PA1274  PA1289  PA1299  PA1314  PA1325  PA1501  PA1503  PA1508  PA1516 17  PA1567 68  PA3263  PA3663  PA3897  PA4924
NA


title: PAO1-WT-1-lane5

description:
WT control for  PA0012  PA0039  PA0045  PA0168  PA0234  PA0310  PA0318  PA0329  PA0351  PA0356  PA0370  PA0383  PA0398  PA0454  PA0495  PA0545  PA0558  PA0568  PA0581  PA0586  PA0625  PA0713  PA0781  PA0952  PA1009  PA1110  PA1190  PA1197  PA1206  PA1208  PA1210  PA1228  PA1332  PA1367  PA1392  PA1412  PA1427  PA1518  PA1527  PA1531  PA1766  PA1817  PA2043  PA2107  PA2117  PA2122  PA2498  PA2548  PA2722 24  PA2727 28  PA2786  PA3784 85  PA3789  PA3796  PA3829  PA3843  PA3846  PA3848  PA3884  PA3886  PA3943  PA3962  PA3969  PA4338  PA4340  PA4362  PA4371 73  PA4384  PA4390  PA4391  PA4394  PA4399  PA4404  PA4422  PA4437  PA4452 54  PA4473  PA4474 76  PA4507  PA4518  PA4629  PA4734
NA


title: PAO1-WT-1-lane4

description:
WT control for PA0068  PA0238  PA0239  PA0269  PA0659  PA0695  PA0793  PA0818  PA0833  PA0937  PA0990  PA1050  PA1075  PA1123  PA1126  PA1679  PA1743  PA1749  PA1753  PA1761  PA1784  PA1789  PA1834  PA1840  PA1874  PA1885  PA1887-88  PA1889  PA1891-97  PA1921  PA1941  PA1957  PA2049  PA2072  PA3142-44  PA4048-49  PA4105-06  PA4141  PA4517  PA4531  PA4539  PA4543  PA4575  PA4611
NA


title: PAO1-WT-1-lane6

description:
WT control for  PA1424  PA2260  PA2448  PA3248  PA3380  PA4382  PA4634
NA


title: PA4712-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4712.xlsx

value: PA4712 mutant


title: PA4712-2


title: PA4075-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4075.xlsx

value: PA4075 mutant


title: 10 day head wild type biol rep 4

description:
Library name: h.wt.4
R4

value: Head


title: PA4689-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4689.xlsx

value: PA4689 mutant


title: PA4075-2


title: PA4689-1


title: PA4577-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4577.xlsx

value: PA4577 mutant


title: PA4577-1


title: PA4509-11-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4509-11.xlsx

value: PA4509-11 mutant


title: PA4485-86-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4485-86.xlsx

value: PA4485-86 mutant


title: PA4509-11-2


title: PA4128-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4128.xlsx

value: PA4128 mutant


title: PA4128-2


title: PA4485-86-1


title: PA3998-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3998.xlsx

value: PA3998 mutant


title: PA3967-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3967.xlsx

value: PA3967 mutant


title: PA3998-1

value: Pseudomonas aeruginosa PAO1


title: PA3967-1


title: PA3964-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3964.xlsx

value: PA3964 mutant


title: PA3756-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3756.xlsx

value: PA3756 mutant

value: grow until mid-log phase in LB


title: PA3964-2


title: PA3698-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3698.xlsx

value: PA3698 mutant


title: PA3756-1


title: PA3698-1


title: PA3612-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3612.xlsx

value: PA3612 mutant


title: PA3612-1


title: PA3325-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3325.xlsx

value: PA3325 mutant


title: PA3325-1


title: PA3218-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3218.xlsx

value: PA3218 mutant


title: PA3359-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3359.xlsx

value: PA3359 mutant


title: PA3359-1


title: PA3218-1


title: PA3207-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3207.xlsx

value: PA3207 mutant


title: PA2880-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2880.xlsx

value: PA2880 mutant


title: PA3207-1


title: PA2807-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2807.xlsx

value: PA2807 mutant


title: PA2807-1


title: PA2880-2


title: PA2793-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2793.xlsx

value: PA2793 mutant


title: PA2793-1


title: PA2682-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2682.xlsx

value: PA2682 mutant


title: PA2627-28-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2627-28.xlsx

value: PA2627-28 mutant


title: PA2627-28-1


title: PA2544-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2544.xlsx

value: PA2544 mutant


title: PA2544-2


title: PA2485-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2485.xlsx

value: PA2485 mutant


title: PA2485-1

value: Pseudomonas aeruginosa PAO1


title: PA2682-2


title: PA2474-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2474.xlsx

value: PA2474 mutant


title: PA2474-1


title: PA2207-09-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2207-09.xlsx

value: PA2207-09 mutant


title: PA2207-09-1

value: grow until mid-log phase in LB


title: PA2167-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2167.xlsx

value: PA2167 mutant


title: PA2167-1


title: PA2095-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2095.xlsx

value: PA2095 mutant


title: PA2095-1


title: PA1926-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1926.xlsx

value: PA1926 mutant


title: PA1981-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1981.xlsx

value: PA1981 mutant


title: PA1926-1


title: PA1829-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1829.xlsx

value: PA1829 mutant


title: PA1981-1


title: PA1643-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1643.xlsx

value: PA1643 mutant


title: PA1829-1


title: PA1830-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1830.xlsx

value: PA1830 mutant


title: PA1492-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1492.xlsx

value: PA1492 mutant


title: PA1830-2


title: PA1643-1


title: PA1492-1


title: PA1472-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1472.xlsx

value: PA1472 mutant


title: PA1472-1


title: PA1369-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1369.xlsx

value: PA1369 mutant


title: PA1291-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1291.xlsx

value: PA1291 mutant


title: PA1291-2


title: PA1134-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1134.xlsx

value: PA1134 mutant


title: PA0988-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0988.xlsx

value: PA0988 mutant


title: PA0983-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0983.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA0983 mutant


title: PA1065-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1065.xlsx

value: PA1065 mutant


title: PA0988-2

value: grow until mid-log phase in LB


title: PA0955-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0955.xlsx

value: PA0955 mutant


title: PA1065-2


title: PA0955-1


title: PA0925-26-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0925-26.xlsx

value: PA0925-26 mutant


title: PA1134-1


title: PA0983-1


title: PA0856-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0856.xlsx

value: PA0856 mutant


title: PA0868-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0868.xlsx

value: PA0868 mutant


title: PA1369-2


title: PA0827-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0827.xlsx

value: PA0827 mutant


title: PA0832-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0832.xlsx

value: PA0832 mutant


title: PA0777-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0777.xlsx

value: PA0777 mutant


title: PA0827-1


title: PA0856-1


title: PA0832-1


title: PA0777-1


title: PA0702-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0702.xlsx

value: PA0702 mutant


title: PA0702-1


title: PA0624-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0624.xlsx

value: PA0624 mutant


title: PA0624-1


title: PA0566-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0566.xlsx

value: PA0566 mutant


title: PA0560-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0560.xlsx

value: PA0560 mutant


title: PA0474-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0474.xlsx

value: PA0474 mutant


title: PA0474-1


title: PA0469-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0469.xlsx

value: PA0469 mutant


title: PA0469-2

value: Pseudomonas aeruginosa PAO1


title: PA0566-2


title: PA0560-1


title: PA0278-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0278.xlsx

value: PA0278 mutant


title: Mycosis fungoides patient 9 plaque skin lesion CosMx SMI

status: Public on Jul 07 2026

type: RNA

city: Seoul

first: Myoung Eun

last: Choi

address: Song-pa gu

country: South Korea

institute: Asan medical center

description: CosMx SMI profiling of MF plaque stage skin, patient 9

hyb_protocol: In situ hybridization was performed on FFPE sections according to the NanoString CosMx SMI protocol. Probe hybridization, ligation, and fluorescence imaging were performed on the CosMx SMI instrument.

scan_protocol: Fluorescence imaging was performed on the NanoString CosMx SMI instrument. Multiple fields of view (FOVs) were acquired per tissue section. Transcript detection and cell segmentation were performed using NanoString AtoMx software.

data_processing:
Raw transcript counts were processed using NanoString AtoMx software. Cell segmentation was performed using DAPI and morphology marker channels. Downstream analysis including quality control, normalization (SCTransform), dimensionality reduction, and cell type annotation was performed in R using Seurat v5. Cells passing QC filters (nCount_RNA > 0, qcFlagsRNACounts = Pass) were retained for analysis.
Raw transcript counts per cell per gene

source_name: skin biopsy

label_protocol: RNA targets were detected using the NanoString CosMx 980-plex RNA panel with fluorescently labeled probes according to the manufacturer's protocol (NanoString Technologies).

growth_protocol: N/A - clinical biopsy specimens

extract_protocol: Skin punch biopsies from patients with mycosis fungoides were formalin-fixed and paraffin-embedded (FFPE). FFPE sections (5 um) were prepared for CosMx SMI profiling according to the NanoString CosMx SMI FFPE sample preparation protocol.

treatment_protocol: N/A - clinical biopsy specimens

tag: disease

value: mycosis fungoides

value: skin

tag: disease stage

value: plaque

tag: patient id


title: PETCC2610, DOX+PeptideE, rep2

city: Wuhu

first: Yu

last: Du

address: No. 8, Yinhe Avenue, Fanchang Economic Development Zone, Fanchang District

country: China

institute: Nourse Centre for Pet Nutrition

description: Library name: DOX_taiE2

data_processing:
Raw sequencing reads (FASTQ format) were quality-controlled using FastQC (v0.11.9). Low-quality reads and adapter sequences were trimmed using fastp (v0.19.5) with default parameters.
Assembly: Felis catus reference genome assembly F.catus_Fca126_mat1.0 (GCF_018350175.1)
Supplementary files format and content: Processed data are provided as a tab-delimited text file containing the gene expression count matrix for all six samples. Columns include gene ID, gene name, gene description, and raw read counts for each sample (DOX1, DOX2, DOX3, DOX_taiE1, DOX_taiE2, DOX_taiE3).

organism: Felis catus

source_name: kidney

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (TIANGEN; Cat. No. DP424) according to the manufacturer's instructions. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated by agarose gel electrophoresis and Agilent 5300 (RIN > 6.5).
mRNA was enriched from total RNA using Oligo(dT)-coated magnetic beads. The enriched mRNA was fragmented into approximately 300 bp fragments using fragmentation buffer. First-strand cDNA was synthesized using random primers and reverse transcriptase, followed by second-strand cDNA synthesis to generate double-stranded cDNA. The cDNA products were end-repaired, A-tailed, and ligated with sequencing adaptors. The adaptor-ligated products were purified and size-selected, followed by PCR amplification to enrich the final library. Library quality was assessed, and sequencing was performed on the Illumina NovaSeq 6000 platform (paired-end 150 bp).

value: kidney

value: PETCC 2610

value: DOX+PeptideE


title: PA0200-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0200.xlsx

value: PA0200 mutant

value: grow until mid-log phase in LB


title: PA0278-2


title: PA0200-1


title: PA0112-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0112.xlsx

value: PA0112 mutant


title: PA0112-2


title: PA0104-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0104.xlsx

value: PA0104 mutant


title: PA0104-1


title: PA0052-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0052.xlsx

value: PA0052 mutant


title: PA0038-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0038.xlsx

value: PA0038 mutant


title: PA0038-1


title: PA5061-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA5061.xlsx

value: PA5061 mutant


title: PA5061-1


title: PA0052-1


title: PA5027-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA5027.xlsx

value: PA5027 mutant


title: PA5027-1


title: PA4863-68-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4863-68.xlsx

value: PA4863-68 mutant


title: PA4863-68-1

value: Pseudomonas aeruginosa PAO1


title: PA4630-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4630.xlsx

value: PA4630 mutant


title: PA4630-2


title: PA4573-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4573.xlsx

value: PA4573 mutant


title: PA4573-1


title: PA4467-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4467.xlsx

value: PA4467 mutant


title: PA4467-1


title: PA4383-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4383.xlsx

value: PA4383 mutant


title: PA4360-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4360.xlsx

value: PA4360 mutant


title: PA4327-28-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4327-28.xlsx

value: PA4327-28 mutant


title: PA4360-1


title: PA4327-28-1


title: PA4383-2


title: PA4121-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4121.xlsx

value: PA4121 mutant


title: PA4121-1


title: PA4111-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4111.xlsx

value: PA4111 mutant


title: PA4111-2

value: grow until mid-log phase in LB


title: PA4099-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4099.xlsx

value: PA4099 mutant


title: PA4099-2


title: PA4095-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4095.xlsx

value: PA4095 mutant


title: PA4095-2


title: PA4093-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4093.xlsx

value: PA4093 mutant


title: PA4071-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4071.xlsx

value: PA4071 mutant


title: PA4093-2


title: PA3762-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3762.xlsx

value: PA3762 mutant


title: PA4071-1


title: PA3727-28-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3727-28.xlsx

value: PA3727-28 mutant


title: PA3727-28-1


title: PA3762-1


title: PA3726-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3726.xlsx

value: PA3726 mutant


title: PA3726-1

value: Pseudomonas aeruginosa PAO1


title: PA3661-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3661.xlsx

value: PA3661 mutant


title: PA3616-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3616.xlsx

value: PA3616 mutant


title: PA3616-1


title: PA3564-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3564.xlsx

value: PA3564 mutant


title: PA3564-1


title: PA3472-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3472.xlsx

value: PA3472 mutant


title: PA3451-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3451.xlsx

value: PA3451 mutant


title: PA3472-1


title: PA3451-1


title: PA3304-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3304.xlsx

value: PA3304 mutant


title: PA3304-1


title: PA3301-02-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3301-02.xlsx

value: PA3301-02 mutant


title: PA3216-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3216.xlsx

value: PA3216 mutant


title: PA3301-02-2

value: grow until mid-log phase in LB


title: PA3216-1


title: PA3208-09-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3208-09.xlsx

value: PA3208-09 mutant


title: PA3208-09-1


title: PA3012-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3012.xlsx

value: PA3012 mutant


title: PA2927-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2927.xlsx

value: PA2927 mutant


title: PA3012-1


title: PA2927-1


title: PA2847-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2847.xlsx

value: PA2847 mutant


title: PA2847-1


title: PA2695-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2695.xlsx

value: PA2695 mutant


title: PA2660-61-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2660-61.xlsx

value: PA2660-61 mutant


title: PA2695-1


title: PA2487-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2487.xlsx

value: PA2487 mutant


title: PA2487-1

value: Pseudomonas aeruginosa PAO1


title: PA2328-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2328.xlsx

value: PA2328 mutant


title: PA2660-61-1


title: PA2328-1


title: PA2179-80-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2179-80.xlsx

value: PA2179-80 mutant


title: PA2179-80-1


title: PA2618-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2618.xlsx

value: PA2618 mutant


title: PA2618-1


title: PA1860-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1860.xlsx

value: PA1860 mutant


title: PA1860-1


title: PA1522-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1522.xlsx

value: PA1522 mutant


title: PA1522-1


title: PA1499-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1499.xlsx

value: PA1499 mutant


title: PA0855-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0855.xlsx

value: PA0855 mutant


title: PA1499-1


title: PA0855-1


title: PA0556-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0556.xlsx

value: PA0556 mutant


title: PA0556-2

value: grow until mid-log phase in LB


title: PA0462-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0462.xlsx

value: PA0462 mutant


title: PA0267-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0267.xlsx

value: PA0267 mutant


title: PA0462-1


title: PA0267-1


title: PA0135-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0135.xlsx

value: PA0135 mutant


title: PA0135-1


title: PA0116-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0116.xlsx

value: PA0116 mutant


title: PA0116-1


title: PA0057-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0057.xlsx

value: PA0057 mutant


title: PA0057-2


title: PA4849-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4849.xlsx

value: PA4849 mutant


title: PA4849-2


title: PA4840-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4840.xlsx

value: PA4840 mutant


title: PA4840-1

value: Pseudomonas aeruginosa PAO1


title: PA4087-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4087.xlsx

value: PA4087 mutant


title: PA4065-66-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4065-66.xlsx

value: PA4065-66 mutant


title: PA4087-1


title: PA4045-46-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4045-46.xlsx

value: PA4045-46 mutant


title: PA4065-66-1


title: PA4045-46-1


title: PA4038-40-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4038-40.xlsx

value: PA4038-40 mutant


title: PA4038-40-1


title: PA4028-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4028.xlsx

value: PA4028 mutant


title: PA4028-1


title: PA4017-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4017.xlsx

value: PA4017 mutant


title: PA4017-1


title: PA4015-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4015.xlsx

value: PA4015 mutant


title: PA4015-1


title: PA4010-11-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4010-11.xlsx

value: PA4010-11 mutant


title: PA4010-11-1

value: grow until mid-log phase in LB


title: PA3892-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3892.xlsx

value: PA3892 mutant


title: PA3892-1


title: PA3791-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3791.xlsx

value: PA3791 mutant


title: PA3772-73-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3772-73.xlsx

value: PA3772-73 mutant


title: PA3772-73-1


title: PA3765-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3765.xlsx

value: PA3765 mutant


title: PA3791-1


title: PA3765-1


title: PA3578-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3578.xlsx

value: PA3578 mutant


title: PA3578-1


title: PA3572-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3572.xlsx

value: PA3572 mutant


title: PA3572-1


title: PA3539-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3539.xlsx

value: PA3539 mutant


title: PA3539-1

value: Pseudomonas aeruginosa PAO1


title: PA3313-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3313.xlsx

value: PA3313 mutant


title: PA3313-1


title: PA3287-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3287.xlsx

value: PA3287 mutant


title: PA3287-2


title: PA3281-84-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3281-84.xlsx

value: PA3281-84 mutant


title: PA3281-84-1


title: PA3255-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3255.xlsx

value: PA3255 mutant


title: PA3231-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3231.xlsx

value: PA3231 mutant


title: PA2736-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2736.xlsx

value: PA2736 mutant


title: PA3255-1


title: PA2736-1


title: PA3231-2


title: PA2609-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2609.xlsx

value: PA2609 mutant


title: PA2650-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2650.xlsx

value: PA2650 mutant


title: PA2609-1

value: grow until mid-log phase in LB


title: PA2650-2


title: PA2569-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2569.xlsx

value: PA2569 mutant


title: PA2595-96-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2595-96.xlsx

value: PA2595-96 mutant


title: PA2595-96-2


title: PA2569-1


title: PA2496-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2496.xlsx

value: PA2496 mutant


title: PA2451-52-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2451-52.xlsx

value: PA2451-52 mutant


title: PA2451-52-1


title: PA2440-41-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2440-41.xlsx

value: PA2440-41 mutant


title: PA2178-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2178.xlsx

value: PA2178 mutant


title: PA1640-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1640.xlsx

value: PA1640 mutant


title: PA1640-1

value: Pseudomonas aeruginosa PAO1


title: PA1620-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1620.xlsx

value: PA1620 mutant


title: PA1620-1


title: PA1506-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1506.xlsx

value: PA1506 mutant


title: PA1506-1


title: PA1381-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1381.xlsx

value: PA1381 mutant


title: PA1378-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1378.xlsx

value: PA1378 mutant


title: PA1378-1


title: PA0925-26-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0925-26.xlsx

value: PA0925-26 mutant


title: PA1209-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1209.xlsx

value: PA1209 mutant


title: PA1195-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1195.xlsx

value: PA1195 mutant


title: PA1191-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1191.xlsx

value: PA1191 mutant


title: PA1195-1

value: grow until mid-log phase in LB


title: PA1181-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1181.xlsx

value: PA1181 mutant


title: PA1135-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1135.xlsx

value: PA1135 mutant


title: PA1088-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1088.xlsx

value: PA1088 mutant


title: PA1044-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1044.xlsx

value: PA1044 mutant


title: PA1135-2


title: PA0758-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0758.xlsx

value: PA0758 mutant


title: PA0741-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0741.xlsx

value: PA0741 mutant


title: PA4875-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4875.xlsx

value: PA4875 mutant


title: PA0741-1

value: Pseudomonas aeruginosa PAO1


title: PA4870-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4870.xlsx

value: PA4870 mutant


title: PA4623-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4623.xlsx

value: PA4623 mutant


title: PA4870-1


title: PA3661-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3661.xlsx

value: PA3661 mutant


title: PA4617-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4617.xlsx

value: PA4617 mutant


title: PA4617-2


title: PA3755-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3755.xlsx

value: PA3755 mutant


title: PA3752-54-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3752-54.xlsx

value: PA3752-54 mutant


title: PA3755-1


title: PA3752-54-1


title: PA3730-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3730.xlsx

value: PA3730 mutant


title: PA3730-1


title: PA3705-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3705.xlsx

value: PA3705 mutant


title: PA3681-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3681.xlsx

value: PA3681 mutant

value: grow until mid-log phase in LB


title: PA3681-1


title: PA3496-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3496.xlsx

value: PA3496 mutant


title: PA4623-1


title: PA3496-1


title: PA3489-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3489.xlsx

value: PA3489 mutant


title: PA3489-1


title: PA3453-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3453.xlsx

value: PA3453 mutant


title: PA3453-2


title: PA3436-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3436.xlsx

value: PA3436 mutant


title: PA3422-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3422.xlsx

value: PA3422 mutant


title: PA3705-2


title: PA3390-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3390.xlsx

value: PA3390 mutant


title: PA3422-1

value: Pseudomonas aeruginosa PAO1


title: PA3390-1


title: PA3374-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3374.xlsx

value: PA3374 mutant


title: PA3374-1


title: PA3372-73-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3372-73.xlsx

value: PA3372-73 mutant


title: PA2440-41-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2440-41.xlsx

value: PA2440-41 mutant


title: PA2496-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2496.xlsx

value: PA2496 mutant


title: PA1644-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1644.xlsx

value: PA1644 mutant


title: PA2178-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2178.xlsx

value: PA2178 mutant


title: PA1644-2


title: PA3372-73-1


title: PA3335-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3335.xlsx

value: PA3335 mutant


title: PA3335-1


title: PA1381-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1381.xlsx

value: PA1381 mutant


title: PA3322-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3322.xlsx

value: PA3322 mutant


title: PA3322-2

value: grow until mid-log phase in LB


title: PA3317-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3317.xlsx

value: PA3317 mutant


title: PA3317-2


title: PA3306-07-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3306-07.xlsx

value: PA3306-07 mutant


title: PA1209-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1209.xlsx

value: PA1209 mutant


title: PA3289-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3289.xlsx

value: PA3289 mutant


title: PA3306-07-2


title: PA1191-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1191.xlsx

value: PA1191 mutant


title: Patient 653  009 stroma

city: Montreal

first: Tamiko

last: Nishimura

address: 740 ave Dr Penfield

country: Canada

institute: McGill University

description: Library name: 9_WTA_PanCK_CD68 | 009 | stroma

library_source: other

data_processing:
The raw data (FASTQ) was converted to DCC files for upload into Bruker Spatial's proprietary software. Data was Q3 normalized and target mRNAs that were detected in at least 1% of the AOIs were retained in the analysis, resulting in inclusion of 12,489 targets.
Assembly: Nanostring synthetic WTA and custom respiratory microbe barcode reference
Supplementary files format and content: Q3 normalized count matrix table for 184 libraries with 12,489 targets
Library strategy: Spatial Transcriptomics

molecule: other

source_name: lung needle biopsy

extract_protocol:
Clinical biopsies were fixed in formalin, embedded in paraffin, and sectioned onto positively charged slides (4 biopsies per slide) for GeoMx DSP WTA analysis. Barcodes attached to antisense probes were released by UV-illumination and collected.
Releasates from each area-of-illumination (PanCK+ or PanCK-/stroma) were collected into a well of a 96-well plate and dual-index Illumina sequencing adapters were added by PCR amplification. Libraries were pooled and sequenced on an Illumina NovaSeq 6000.

value: lung needle biopsy

value: Female

tag: caucasian

value: Yes

tag: bmi

tag: diagnosis (asthma_or_healthy_control)

value: Asthma

tag: asthma severity

value: Severe

tag: ever smoked

value: No


title: PA3289-1

value: Pseudomonas aeruginosa PAO1


title: PA3270-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3270.xlsx

value: PA3270 mutant


title: PA3270-1


title: PA3259-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3259.xlsx

value: PA3259 mutant


title: PA1181-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1181.xlsx

value: PA1181 mutant


title: PA3259-1


title: PA3241-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3241.xlsx

value: PA3241 mutant


title: PA1044-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1044.xlsx

value: PA1044 mutant

value: grow until mid-log phase in LB


title: PA3240-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3240.xlsx

value: PA3240 mutant


title: PA3241-1


title: PA1088-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1088.xlsx

value: PA1088 mutant


title: PA3240-1


title: PA2806-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2806.xlsx

value: PA2806 mutant


title: PA2729-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2729.xlsx

value: PA2729 mutant


title: PA2729-2


title: PA2705-07-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2705-07.xlsx

value: PA2705-07 mutant


title: PA2705-07-2


title: PA2699-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2699.xlsx

value: PA2699 mutant


title: PA0758-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0758.xlsx

value: PA0758 mutant


title: PA2699-1


title: PA2668-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2668.xlsx

value: PA2668 mutant


title: PA2668-1


title: PA2625-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2625.xlsx

value: PA2625 mutant


title: PA2625-1


title: PA2613-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2613.xlsx

value: PA2613 mutant


title: PA2613-2

value: Pseudomonas aeruginosa PAO1


title: PA2589-90-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2589-90.xlsx

value: PA2589-90 mutant


title: PA2589-90-2


title: PA2581-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2581.xlsx

value: PA2581 mutant


title: PA2576-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2576.xlsx

value: PA2576 mutant


title: PA2581-1


title: PA2576-1


title: PA2575-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2575.xlsx

value: PA2575 mutant


title: PA2575-1


title: PA2503-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2503.xlsx

value: PA2503 mutant


title: PA2437-39-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2437-39.xlsx

value: PA2437-39 mutant

value: grow until mid-log phase in LB


title: PA2503-2


title: PA2437-39-1


title: Patient 660  005 stroma

description: Library name: 9_WTA_PanCK_CD68 | 005 | stroma

value: lung needle biopsy

value: Female

value: Yes

value: Asthma

value: Severe

value: No


title: Patient 656  003 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 003 | PanCK+

value: Male

value: Control

value: Not applicable


title: Patient 674  005 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 674  005 stroma

description: Library name: 10_WTA_PanCK_CD68 | 005 | stroma


title: Patient 670  003 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 003 | PanCK+

value: Non-severe


title: PA4875-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4875.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA4875 mutant


title: PA1625-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1625.xlsx

value: PA1625 mutant


title: PA1625-1


title: PA1293-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1293.xlsx

value: PA1293 mutant


title: PA1730-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1730.xlsx

value: PA1730 mutant


title: PA1016-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1016.xlsx

value: PA1016 mutant


title: PA1016-1

value: grow until mid-log phase in LB


title: PA0820-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0820.xlsx

value: PA0820 mutant


title: PA0820-1


title: PA0749-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0749.xlsx

value: PA0749 mutant


title: PA0742-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0742.xlsx

value: PA0742 mutant


title: PA0742-1


title: PA0348-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0348.xlsx

value: PA0348 mutant


title: PA0485-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0485.xlsx

value: PA0485 mutant


title: PA0498-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0498.xlsx

value: PA0498 mutant


title: PA0485-2


title: PA0047-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0047.xlsx

value: PA0047 mutant


title: PA0348-1


title: PA0498-1


title: PA0047-1


title: PA4929-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4929.xlsx

value: PA4929 mutant


title: PA4926-27-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4926-27.xlsx

value: PA4926-27 mutant


title: PA4830-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4830.xlsx

value: PA4830 mutant


title: PA4929-2

value: Pseudomonas aeruginosa PAO1


title: PA4926-27-1


title: PA4828-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4828.xlsx

value: PA4828 mutant


title: PA4828-1


title: PA4818-20-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4818-20.xlsx

value: PA4818-20 mutant


title: PA4818-20-2


title: PA4830-1


title: PA4802-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4802.xlsx

value: PA4802 mutant


title: PA4802-2


title: PA4815-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4815.xlsx

value: PA4815 mutant


title: PA4782-83-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4782-83.xlsx

value: PA4782-83 mutant


title: PA4753-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4753.xlsx

value: PA4753 mutant

value: grow until mid-log phase in LB


title: PA4792-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4792.xlsx

value: PA4792 mutant


title: PA4721-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4721.xlsx

value: PA4721 mutant


title: PA4782-83-1


title: PA4717-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4717.xlsx

value: PA4717 mutant


title: PA4717-1


title: PA4716-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4716.xlsx

value: PA4716 mutant


title: PA4711-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4711.xlsx

value: PA4711 mutant


title: PA4716-2


title: PA4702-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4702.xlsx

value: PA4702 mutant


title: PA4701-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4701.xlsx

value: PA4701 mutant


title: PA4702-1


title: PA4637-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4637.xlsx

value: PA4637 mutant


title: PA4657-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4657.xlsx

value: PA4657 mutant


title: PA4701-1

value: Pseudomonas aeruginosa PAO1


title: NSWT4

first: Ana Maria

last: Hincapie

address: 1160 Pine avenue West

description: Library name: A004

data_processing:
SALMON
Assembly: MM_grch38_ens94
Supplementary files format and content: .xlsx

organism: Mus musculus

source_name: Isolated B lymphocytes

extract_protocol:
Qiagen Rneasy Plus Universal mini kit
NEBNext Ultra II RNA Library Prep Kit for Illumina

tag: cell type

value: Isolated B lymphocytes

value: Ptpn2wt/wt mb1 Cre+

value: No treatment


title: IFN14_Baseline_cd34pos_sn10x

first: Anna

middle: S.

last: Nam

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

description:
Library name: IFN14_Baseline_cd34pos_sn10x
10x genomics

library_source: genomic single cell

data_processing:
10x data was processed using Cell Ranger 1 and v6.1.2 using default parameters. RNA reads were aligned to the human referece genome. Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, 5) Analyze reads with CB that are also observed in the 10x RNA-seq dataATAC-seq 6) Collapse networks of closely related UMIs within CBs to correct for sequencing error, 7) Matching of CB/UMI pairs found in 10x scRNA-seq data, discarding those matching non-CALR genes and those matching no gene below a supporting read threshold.
CUT&RUN data were down-sampled to have same number of reads across all conditions within the sample replicate to account for difference in sequencing depth. Among the down-sampled reads, low-quality reads were filtered out using Trimmomatic, resulting reads were aligned with hg38 genome with Bowtie2, and PCR duplicates were removed with SAMtools with a previously described workflow. Aligned reads were then used for peak calling with MACS3 with a q-value threshold of 0.01 and reads from IgG antibody as the control. SPI1 over-enrichment in the called peaks was confirmed with Simple Enrichment Analysis (SEA, v5.5.5). Overlapping peaks between replicates of the same condition were kept for further processing. The peaks were processed with multiBamSummary function from deepTools to obtain counts matrix per sample for downstream analysis.
Genotyping data processing was performed according to the previously published instructions and available Gotcha R package. Briefly, initial FASTQ files were filtered based on base quality scores, and the Fastqsplit function was used to split FASTQ files for subsequent parallel computing. Mutations were determined via the BatchMutationCalling function, which identifies reads that are correctly primed, calculates the counts of reads per cell for each specified genotype (i.e., WT, JAK2-V617F).
Assembly: GRCh38
Supplementary files format and content: Processed 10X data is matrix table of gene/peak counts per cell for each sample
Supplementary files format and content: Output matrices processed from genotyping data have two columns: barcodes (BC) and Genotype

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
GoT-IM Extraction Protocol: Cryopreserved bone marrow mononuclear cells approved by the Institutional Review Board of Weill Cornell Medicine were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, Miltenyi Biotec) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. To eliminate experimental batch effects, cells were labelled simultaneously with hashing antibodies with time-point-identifying barcodes using Hashtag Antibodies 1, 2 or 3 (TotalSeq-A, clone LNH-94, Biolegend) for GoT-IM. To link cell identities to expression of cell surface proteins, cells were also incubated with CITE-seq antibodies according to manufacturer protocol (TotalSeq-A, Biolegend). Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Genotyping of Transcriptomes (GoT) was performed by adapting the 10x Genomics platform. FACS-sorted CD34+ cells for each time-point from the same individual were pooled, targeting a total of 10,000-15,000 cells.  GoT-ATAC Extraction Protocol: Cryopreserved bone marrow mononuclear cells were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, MACS) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Nuclei were isolated from DAPI-, CD34+ cells according to 10x Genomics Demonstrated Low Cell Input Nuclei Isolation protocol. Lysis buffer was prepared following manufacturer’s recommendations and then split into aliquots for each serial sample. Either TotalSeq-A Anti-Nuclei Pore Complex Proteins Hashtag 9 or 10 Antibody (1uL at 1:5 dilution; BioLegend) was added to each aliquot of lysis buffer. Low-input nuclei isolation was otherwise performed following manufacturer’s recommendations. Subsequently, nuclei from each time-point were counted and pooled together at approximately equal proportions. For IFN03, additional nuclei from the IFNa-treated sample were available to be run on a separate lane.  RFX3-OE Extraction Protocol: Cells from frozen umbilical cord blood mononuclear cells were thawed rapidly at 37°C, red blood cell lysis was performed using ACK Lysis Buffer, then centrifuged, and cell pellet was resuspended in cold MACS buffer. Cells were centrifuged at 300g for 5min at 4°C, and resuspended in cold MACs buffer at a concentration of 1x10^7 cells/mL. CD34+ cells were then isolated with the EasySep™ Human CD34 Positive Selection Kit II (StemCell Technologies #17856) according to manufacturer’s protocol. After isolation, cells were counted and plated in 96-well round-bottom plates (Falcon) in StemSpan™ SFEM II media (StemCell Technologies) with StemSpan™ CD34+ Expansion Supplement (StemCell Technologies) and 1% Pen/Strep. After 24 hours in culture, cells were spun down and resuspended in minimal media consisting of StemSpan StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement, 1% Pen/Strep, 10μM prostaglandin E2 (StemCell Technologies #72192) and 100ng/μl poloxamer 407 (Millipore Sigma P2164030). Cells were split into 2 technical replicates each for untransduced condition, mCherry-control vector transduction, and RFX3-OE vector transduction. Lentivirus or PBS control was added at an MOI of 100, spinoculated at 300g, 32°C for 1 hour, and cells were incubated in same lentivirus-containing media for 24 hours at 37°C before resuspension in fresh media consisting of StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement and 1% Pen/Strep. After 48 hours of incubation, cells were stained with CD34-APC antibody (1:50). Cells were then FACS isolated for the CD34+ population in the untransduced condition and the CD34+ mCherry+ populations in the RFX3-OE and mCherrycontrol conditions. Three independent transduction experiments were completed with new units of umbilical cord blood cells. Untransduced, mCherry-Control, and RFX3-OE CD34+ cells were stained with Cell Hashing antibodies (HTO TotalSeq-A, BioLegend) for 30 min at 4°C. Cells were then washed with FACs Buffer three times, pooled, and counted for loading. scRNA-sequencing was then performed using the 10x 3’ v3.1 platform according to manufacturer’s protocol. HTO demultiplexing and downstream analyses such as differential gene expression and gene set enrichment were performed as in GoT-IM for CD34+ bone marrow samples. scRNA-seq experiment was completed on one replicate of three independent transduction experiments.  CUT&RUN Extraction Protocol: UT7 cell lines expressing MPL (thrombopoietin receptor) and either the mutant CALR (type 1, L367Tfs*46) or wildtype CALR transgene (93) were seeded in 10cm plates in DMEM supplemented with 10% FBS (Thomas Scientific) and 5 ng/ml GM-CSF (Miltenyi-Biotec). Cells were treated with 0.1μg/ml Recombinant Human IFN-alpha2a (RC217-14) or PBS-1X control for 24hrs. After treatment, cells were washed 1x with PBS and collected for use with the CUTANA™ CUT&RUN assay (EpiCypher) according to the manufacturer’s protocol. 0.5μg of anti-human rabbit monoclonal PU.1 antibody (ab76543) and IgG antibody (ab172730) were used in the assay.
GoT-IM Library Construction Protocol: The standard 10x Genomics Chromium 3′ (v.3.1 chemistry) was implemented according to the manufacturer’s recommendations up to the cDNA amplification step (10X Genomics, Pleasanton, CA). After cDNA amplification and SPRI cleanup, 10x scRNA-seq and ADT/HTO libraries were generated as recommended. A portion of the cDNA was used for somatic genotyping. Briefly, to capture the somatic genotypes of cells, cDNA was amplified with a locus-specific amplification (10 PCR cycles), using the generic forward SI-PCR primer and a following locus-specific reverse primer for the CALR mutations. The amplified locus-specific cDNAs are then cleaned using SPRI purification to remove unincorporated primers. Finally, the targeted amplicon libraries are generated through a PCR performed with a P5 generic forward PCR primer together with an RPI-x primer. The targeted amplicon libraries were spiked into the remainder of the gene expression and immunophenotyping libraries to be sequenced together on a NovaSeq (Illumina, San Diego, CA). The cycle settings were as follows: 28 cycles for Read 1, 90 cycles for Read 2, 8 cycles for i7 sample index and 8 cycles for i5 sample index.  GoT-ATAC Library Construction Protocol: Single-nucleus gene expression (GEX) and chromatin accessibility libraries were constructed from the pooled nuclei according to the Chromium Next GEM Single Cell Multiome User Guide (10X Genomics). Genotyping libraries targeting the CALR mutant transcripts were constructed from the remaining amplified cDNA, similar to the original GoT method. The re-amplified sample was purified and concentrated via 0.7X SPRI cleanup, eluting it into 10uL Buffer EB. To pre-enrich the CALR mutation locus, a gene-specific PCR was performed with 3uL of cleaned re-amplified cDNA and Partial Read 1 and gene-specific primers. CALR locus-specific amplification was then performed with 3uL of cleaned gene-specific amplified cDNA and SI-PCR and loci-specific Primers. A 0.7X SPRI cleanup was performed, and cDNA was eluted into 11uL Buffer EB. Finally, to construct the targeted amplicon library, loci-amplified cDNA was mixed with P5 Generic and RPIx indexing primers and amplified. The constructed library was cleaned via 0.8X SPRI cleanup and eluted into 12uL Buffer EB. At the cDNA amplification stage of the Chromium Next GEM Single Cell Multiome protocol, supernatant from the 0.6X size selection was retained and was used to generate the hashing libraries as per HTO protocol25 with the following modification. For the hashing library construction step, the PCR reaction was prepared with 0.65uL of 10uM SI-PCR primer, 0.65uL of 10uM TruSeq DNA D7xx_s primer, 11.25uL cleaned supernatant and 12.5 uL Kapa HiFI HotStart Ready Mix (Roche, Basel, Switzerland). Hashing, gene expression, and genotyping libraries were pooled and sequenced together on a NovaSeq (Illumina).  Genotyping for JAK2-mutated samples (IFN14, IFN15): Nuclei were processed according to the 10x Genomics Chromium Next GEM Single-Cell ATAC v2 Kit guidelines, with several modifications specific to the GoT-ChA protocol. 1 µl of 22.5 µM GoT–ChA primer mix was added to the barcoding reaction mixture, containing the locus-specific primers GoT–ChA_R1N and GoT–ChA_Rev (primer sequences in Supplementary Table 32). During the post-GEM incubation clean-up, 45.5 µl of elution solution I was used to elute the SPRIselect bead reaction, and 5 µl was used for GoT-ChA library generation. GoT-ChA libraries were generated according to the published protocol.

value: Bone marrow

tag: disease state

value: Polycythemia vera

tag: treatment

value: Control


title: PA4657-2

tag: tissue

value: grow until mid-log phase in LB


title: PA4637-1


title: PA4618-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4618.xlsx

value: PA4618 mutant


title: IFN14_24months_cd34pos_sn10x

description:
Library name: IFN14_24months_cd34pos_sn10x
10x genomics

value: IFNa


title: PA4586-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4586.xlsx

value: PA4586 mutant


title: PA3941-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3941.xlsx

value: PA3941 mutant


title: PA3787-88-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3787-88.xlsx

value: PA3787-88 mutant


title: PA3959-60-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3959-60.xlsx

value: PA3959-60 mutant


title: PA1730-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1730.xlsx

value: PA1730 mutant


title: PA1293-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1293.xlsx

value: PA1293 mutant


title: PA3786-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3786.xlsx

value: PA3786 mutant


title: PA3688-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3688.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA3688 mutant


title: PA3674-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3674.xlsx

value: PA3674 mutant


title: PA3674-2


title: PA0749-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0749.xlsx

value: PA0749 mutant


title: PA3662-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3662.xlsx

value: PA3662 mutant


title: PA3618-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3618.xlsx

value: PA3618 mutant


title: PA3618-1


title: PA3436-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3436.xlsx

value: PA3436 mutant


title: PA3614-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3614.xlsx

value: PA3614 mutant

value: grow until mid-log phase in LB


title: PA3614-2


title: PA3613-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3613.xlsx

value: PA3613 mutant


title: PA4815-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4815.xlsx

value: PA4815 mutant


title: PA3613-1


title: PA4792-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4792.xlsx

value: PA4792 mutant


title: PA4753-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4753.xlsx

value: PA4753 mutant


title: Bone marrow, MSC, 21-Day Tenogenic differentiation

city: Rochester

first: Hani

middle: A

last: Awad

state: NY

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

description: Library name: BM-MSC_TenoDiff

data_processing:
Samples were aligned using CellRanger 8.0.0 using default parameters
Sequencing Platform - Illumina NovaSeqX Plus
Data Formatting - bcl-convert 4.1.7
Assembly: GRCh38
Supplementary files format and content: h5 filtered feature barcode matrix

growth_protocol: Primary fibroblasts were grown on tissue-culture treated plastic in MEM-alpha supplemented with 2% FBS, 1% pen-strep, and 55 microM 2-Mercaptoethanol. BM-MSCs and iMPCs were grown on tissue-culture treated plastic coated with ACF Cell Attachment Substrate (STEMCELL Technologies) in MesenCult-ACF Plus Media (STEMCELL Technologies). Cells were grown to 95% confluency prior to 21-day, 7-day, or tenogenic differentiation culture. At the end of culture, all cells were passaged with ACF Cell Dissociation Kit (STEMCELL Technologies) and resuspended as single cells prior to sequencing.

extract_protocol:
Extraction is included within the 10X genomics scRNA protocol
Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification.

treatment_protocol: Tenogenic differentiation was performed using materials from STEMCELL Technologies. On day 0, cells were treated with a differentiation media A. This was changed to a differentiation media B on day 3. Media was refreshed every 2-3 days for the remaining culture period until day 21.

value: Bone marrow

value: Mesenchymal stromal cell

value: Tenogenic differentiation


title: PA3575-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3575.xlsx

value: PA3575 mutant


title: PA4718-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4718.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA4718 mutant


title: PA4721-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4721.xlsx

value: PA4721 mutant


title: PA4718-2


title: PA3532-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3532.xlsx

value: PA3532 mutant


title: stomach male control rep4

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: OCSPP

institute: US EPA

description: Library name: S_04

data_processing:
RNA-seq data quality was assessed using FASTQC (v0.12.1) and summarized with MultiQC (v1.28)
PCR duplicates were removed by deduplicating sequencing reads with UMI-tools (v1.1.5)
Low-quality bases were trimmed using Cutadapt (v4.9) and Trim Galore (v0.6.10)
The cleaned reads were then aligned to the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1) using STAR (v2.7.11b)
Quantification of transcript abundance was performed with Salmon (v1.10.3)
Assembly: the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcrit level generated by salmon  (*.gene_counts.tsv )
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcript level generated by salmon  (*.transcript_counts.tsv )

organism: Rattus norvegicus

source_name: stomach

growth_protocol: Rats were fed a standard rodent chow

extract_protocol:
A 50% (v/v) solution of Antifoam A (cat. no. A5633; Sigma, St. Louis, MO) was prepared in propylene glycol (cat. no. W294004; Sigma St. Louis, MO). The solution was vortexed prior to use. Homogenization buffer was prepared by adding 10 µl of β-mercaptoethanol (cat no. 0482, VWR, Radnor, PA) and 60 µl antifoam solution per milliliter of Buffer RLT Plus (Qiagen, Germantown, MD).
Prior to homogenization, large tissue samples were broken into smaller pieces using a mortar and pestle cooled with liquid nitrogen (LN2). Several of the resulting pieces (each approximately 3–5 mm) were then pulverized together to produce the final sample. For homogenization, 400 µl of buffer was added to a 3 ml, flat-bottom polystyrene tube (Globe Scientific, Mahwah, NJ). The tube was placed into a CoolRack CF15 (Corning Inc., Corning, NY) cooled with LN2. A cooled 30 µl plastic scoop was used to transfer pulverized tissue to the tube. The target mass of tissue was 50 µg, although the actual mass varied due to the need to work quickly and differences in the sizes of the pulverized samples.
The tube was placed on ice, and 600 µl of ice-cold homogenization buffer was added to the sample. The sample was homogenized using a model 985-370 TissueTearor rotor-stator homogenizer with a 7 mm probe (BioSpec Products, Bartlesville, OK) until no remnants of intact tissue were visible. If the homogenate appeared significantly darker than other samples, suggesting an excess of tissue, additional buffer was added until the color of the sample was similar to that of the other samples. Homogenates were stored at -80 °C until used for RNA isolation. The homogenizer was rinsed between samples within a treatment by running it at the highest speed for 30 s in three changes of deionized water. Between treatments, the rotor and stator were disassembled and cleaned with a polyester test tube brush before rinsing in water.
For RNA isolation, homogenized samples were removed from the freezer and placed on ice to thaw. The samples were vortexed, and 100 µl of the homogenate was transferred to the well of a 96-well round bottom plate (Caplugs Evergreen, Buffalo, NY). RNA was isolated using the MagMAX-96 Total RNA Isolation Kit (Fisher Scientific, Hampton, NH) according to the manufacturer’s protocol, except for the substitution of RLT Plus buffer for the lysis/binding solution as described above.
Isolated RNA was quantified on a Synergy HTX plate reader using a Take3 microvolume plate (Agilent, Santa Clara, CA). The integrity of the RNA was analyzed on an Agilent TapeStation using RNA Screen Tapes and reagents (Agilent, Santa Clara, CA). Concentrations of samples ranged from 75 to 470 ng/µl. RNA integrity numbers (RIN) ranged from 8.0 to 10.0; nearly 90% of samples had a RIN higher than 9.0.
Isolated RNA was next used to prepare RNA-Seq libraries. Samples were blocked so that about eight samples of each tissue and treatment combination were included in one of two plates. RNA was normalized to 25 ng/uL with nuclease-free water (Ambion, USA). 250 ng total RNA (10 uL of normalized RNA) was input into mRNA purification with magnetic beads using a PolyA Selection Module (Lexogen, USA). Purified mRNA was then used directly in CORALL mRNA-Seq V2 library preparation with set A unique dual indexes (UDIs). Each batch was checked by qPCR to determine the appropriate number of PCR cycles for library amplification with Add-On PCR V2 kit (Lexogen, USA), SYBR Green (ThermoFisher, USA), and a QuantStudio 6 Flex real-time PCR instrument (ThermoFisher, USA). After final PCR amplification, libraries were quantified with Quant-iT PicoGreen (ThermoFisher, USA). The distribution of library size was checked by TapeStation D1000 assay (Agilent, USA). The average library size was 508 – 517 bp. Samples below 1 ng/uL were re-amplified.

value: stomach

tag: strain

value: Sprague-Dawley

tag: developmental stage

value: adult

value: WT

value: Male-Vehicle Control

value: Batch 2


title: PA3575-1

tag: genotype

value: grow until mid-log phase in LB


title: PA3532-2


title: PA3497-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3497.xlsx

value: PA3497 mutant


title: PA3497-1


title: PA3449-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3449.xlsx

value: PA3449 mutant


title: PA3449-1


title: PA4711-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4711.xlsx

value: PA4711 mutant


title: PA3445-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3445.xlsx

value: PA3445 mutant


title: PA3445-1


title: PA3444-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3444.xlsx

value: PA3444 mutant


title: PA3444-1


title: PA3431-32-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3431-32.xlsx

value: PA3431-32 mutant


title: PA3431-32-1

value: Pseudomonas aeruginosa PAO1


title: PA3403-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3403.xlsx

value: PA3403 mutant


title: PA2819-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2819.xlsx

value: PA2819 mutant


title: PA3403-1


title: PA2869-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2869.xlsx

value: PA2869 mutant


title: PA4627-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4627.xlsx

value: PA4627 mutant


title: PA2819-1


title: PA2817-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2817.xlsx

value: PA2817 mutant


title: PA2869-2


title: PA4627-2


title: PA2817-1


title: PA2805-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2805.xlsx

value: PA2805 mutant


title: PA2805-1


title: PA2752-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2752.xlsx

value: PA2752 mutant


title: stomach male control rep3

description: Library name: S_03

value: stomach

value: Sprague-Dawley

value: adult

value: WT

value: Male-Vehicle Control

tag: batch

value: Batch 3


title: PA4618-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4618.xlsx

value: PA4618 mutant

value: grow until mid-log phase in LB


title: PA4603-06-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4603-06.xlsx

value: PA4603-06 mutant


title: PA4603-06-1

value: Pseudomonas aeruginosa PAO1


title: PA2602-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2602.xlsx

value: PA2602 mutant


title: PA2602-1


title: PA2568-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2568.xlsx

value: PA2568 mutant


title: PA2568-1


title: PA2501-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2501.xlsx

value: PA2501 mutant


title: PA3959-60-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3959-60.xlsx

value: PA3959-60 mutant


title: PA4586-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4586.xlsx

value: PA4586 mutant


title: PA3941-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3941.xlsx

value: PA3941 mutant


title: PA0043-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0043.xlsx

value: PA0043 mutant


title: PA0043-1


title: PA2752-1

value: PA2752 mutant


title: PA5033-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA5033.xlsx

value: PA5033 mutant


title: PA2501-1


title: PA3787-88-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3787-88.xlsx

value: PA3787-88 mutant


title: PA5033-1


title: PA4703-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4703.xlsx

value: PA4703 mutant


title: PA4703-2


title: PA3786-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3786.xlsx

value: PA3786 mutant


title: PA0015-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0015.xlsx

value: PA0015 mutant


title: PA0015-1


title: PA3258-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3258.xlsx

value: PA3258 mutant


title: PA3258-1

value: grow until mid-log phase in LB


title: PA3237-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3237.xlsx

value: PA3237 mutant


title: PA3235-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3235.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA3235 mutant


title: PA3235-1


title: PA3237-2


title: PA3233-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3233.xlsx

value: PA3233 mutant


title: PA3233-1


title: PA3230-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3230.xlsx

value: PA3230 mutant


title: PA3688-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3688.xlsx

value: PA3688 mutant


title: PA3230-1


title: PA3219-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3219.xlsx

value: PA3219 mutant


title: PA3222-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3222.xlsx

value: PA3222 mutant


title: PA3205-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3205.xlsx

value: PA3205 mutant


title: PA3203-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3203.xlsx

value: PA3203 mutant


title: PA3222-1


title: PA3219-1


title: PA2860-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2860.xlsx

value: PA2860 mutant


title: PA2829-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2829.xlsx

value: PA2829 mutant


title: PA2833-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2833.xlsx

value: PA2833 mutant


title: PA2860-2


title: PA2791-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2791.xlsx

value: PA2791 mutant


title: PA2769-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2769.xlsx

value: PA2769 mutant


title: PA2764-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2764.xlsx

value: PA2764 mutant


title: PA2490-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2490.xlsx

value: PA2490 mutant

value: grow until mid-log phase in LB


title: PA2483-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2483.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA2483 mutant


title: PA2490-1


title: PA2483-1


title: PA2471-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2471.xlsx

value: PA2471 mutant


title: PA2450-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2450.xlsx

value: PA2450 mutant


title: PA2436-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2436.xlsx

value: PA2436 mutant


title: PA2464-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2464.xlsx

value: PA2464 mutant


title: PA2434-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2434.xlsx

value: PA2434 mutant


title: PA2434-1


title: PA2471-1


title: PA2380-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2380.xlsx

value: PA2380 mutant


title: PA2380-1


title: PA1471-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1471.xlsx

value: PA1471 mutant


title: PA0977-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0977.xlsx

value: PA0977 mutant


title: PA0670-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0670.xlsx

value: PA0670 mutant


title: PA0585-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0585.xlsx

value: PA0585 mutant


title: PA0585-2


title: PA0553-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0553.xlsx

value: PA0553 mutant


title: PA0553-1


title: PA0543-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0543.xlsx

value: PA0543 mutant


title: PA0541-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0541.xlsx

value: PA0541 mutant


title: PA0526-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0526.xlsx

value: PA0526 mutant


title: PA0522-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0522.xlsx

value: PA0522 mutant

value: grow until mid-log phase in LB


title: PA0526-1

value: Pseudomonas aeruginosa PAO1


title: PA0484-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0484.xlsx

value: PA0484 mutant


title: PA0484-1


title: PA0389-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0389.xlsx

value: PA0389 mutant


title: PA0358-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0358.xlsx

value: PA0358 mutant


title: PA0354-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0354.xlsx

value: PA0354 mutant


title: PA0358-1


title: PA0354-1


title: PA0338-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0338.xlsx

value: PA0338 mutant


title: PA0338-1


title: PA0311-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0311.xlsx

value: PA0311 mutant


title: PA0311-1


title: PA2792-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2792.xlsx

value: PA2792 mutant


title: PA2829-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2829.xlsx

value: PA2829 mutant


title: PA4882-84-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4882-84.xlsx

value: PA4882-84 mutant


title: PA2764-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2764.xlsx

value: PA2764 mutant


title: PA2791-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2791.xlsx

value: PA2791 mutant


title: PA2769-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2769.xlsx

value: PA2769 mutant


title: PA4882-84-1


title: PA2464-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2464.xlsx

value: PA2464 mutant


title: PA2418-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2418.xlsx

value: PA2418 mutant


title: PA2450-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2450.xlsx

value: PA2450 mutant


title: PA4713-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4713.xlsx

value: PA4713 mutant

value: grow until mid-log phase in LB


title: PA4620-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4620.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA4620 mutant


title: PA4377-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4377.xlsx

value: PA4377 mutant